V. Freitas, J. Delgado

Building Pathology and Rehabilitation • 2013

Reducing the Risk of Microbial Growth on Insulated Walls by Improving the Properties of the Surface Materials.- Biological Defacement of External Thermal Insulation Composite Systems (ETICS).- Effectiveness and Durability of Biocides in Building Coatings - Biological Aspects.- Hygrothermal Conditions and Mould Growth Potential in Cold Attics - Impact of Weather, Building System and Construction Design Characteristics.- Controlled Ventilation of Historic Buildings - Assessment of Impact on the Indoor Environment via Hygrothermal Building Simulation.- Degradation Control of Historical Walls with Rising Damp Problems.- Hygrothermal Performance and Damage Risk of Green Roofs.- Applicability of the Pull-Off Test: Teachings from a Large Sample of In-Situ Tests.- Moisture Robustness during Retrofitting of Timber Frame Walls with Vacuum Insulation Panels - Experimental and Theoretical Studies.- Wind Resistance Evaluation to Dynamic Response of Mechanically Anchored Waterproofing Membrane System.-

A. Mackay

Photochemical & Photobiological Sciences • 2022

Antimicrobial photodynamic therapy has become an important component in the treatment of human infection. This review considers historical guidelines, and the scientific literature to envisage what future clinical guidelines for treating skin infection might include. Antibiotic resistance, vertical and horizontal infection control strategies and a range of technologies effective in eradicating microbes without building up new resistance are described. The mechanism of action of these treatments and examples of their clinical use are also included. The research recommendations of NICE Guidelines on the dermatological manifestations of microbial infection were also reviewed to identify potential applications for PDT. The resistance of some microbes to antibiotics can be halted, or even reversed through the use of supplementary drugs, and so they are likely to persist as a treatment of infection. Conventional PDT will undoubtedly continue to be used for a range of skin conditions given existing healthcare infrastructure and a large evidence base. Daylight PDT may find broader antimicrobial applications than just Acne and Cutaneous Leishmaniasis, and Ambulatory PDT devices could become popular in regions where resources are limited or daylight exposure is not possible or inappropriate. Nanotheranostics were found to be highly relevant, and often include PDT, however, new treatments and novel applications and combinations of existing treatments will be subject to Clinical Trials.

J. Ettenauer, V. Jurado, G. Piñar et al.

PLoS ONE • 2014

A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.

G. Sepich-Poore, L. Zitvogel, R. Straussman et al.

Science • 2021

Separating microbes and cancers The role of microorganisms in causing and sustaining cancers has been in dispute for centuries. Through the lens of gut- and tumor-associated microbes, Sepich-Poore et al. review our current understanding of the microbiota in cancer, building a “microbially conscious” framework. The authors argue that humans should be considered as a meta-organism, but how our microbiota influences cancer is still not well understood mechanistically. Nevertheless, advances in microbiome research are improving our understanding of immuno-oncology and driving new diagnostic and therapeutic approaches. Science, this issue p. eabc4552 BACKGROUND Historical accounts linking cancer and microbes date as early as four millennia ago. After establishment of the germ theory of infectious diseases, clinical research of microbial influences on cancer began in 1868, when William Busch reported spontaneous tumor regressions in patients with Streptococcus pyogenes infections. Over the next century, poor reproducibility, erroneous microbiological claims, and severe toxicity led many to discount the role of bacteria in carcinogenesis and cancer therapy. However, these studies provided the first crude demonstrations of cancer immunotherapy. Contemporaneously, the viral theory of cancer flourished, spurred by the 1911 discovery of Rous sarcoma virus, which transformed benign tissue into malignant tumors in chickens. The decades-long search to find viruses behind every human cancer ultimately failed, and many cancers have been linked to somatic mutations. Now the field is encountering intriguing claims of the importance of microbes, including bacteria and fungi, in cancer and cancer therapy. This Review critically evaluates this evidence in light of modern cancer biology and immunology, delineating roles for microbes in cancer by examining advances in proposed mechanisms, diagnostics, and modulation strategies. ADVANCES Few microbes directly cause cancer, but many seem complicit in its growth, often acting through the host’s immune system; conversely, several have immunostimulatory properties. Mechanistic analyses of gut microbiota–immune system interactions reveal powerful effects on antitumor immunity by modulating primary and secondary lymphoid tissue activities. Many of these pathways invoke Toll-like receptor–initiated cytokine signaling, but microbial metabolic effects and antigenic mimicry with cancer cells are also important. In preclinical models, microbial metabolites also regulate phenotypes of tumor somatic mutations and modulate immune checkpoint inhibitor efficacy. Emerging evidence suggests that intratumoral bacteria exist and are active, with overlapping immunohistochemistry, immunofluorescence, electron microscopy, and sequencing data in ~10 cancer types. Preliminary studies further suggest that fungi and bacteriophages contribute to gastrointestinal cancers. However, the abundance of intratumoral microbial cells is low relative to cancer cells, and knowledge of their functional repertoire and potency remains limited. Further validation of their prevalence and impact is needed in diverse cohorts and therapeutic contexts. The immunomodulatory effects of host microbiota have reinvigorated efforts to change their composition as a form of immunotherapy. Despite extensive preclinical evidence, translation of microbiota modulation approaches into humans has not yet materialized into commercialized therapies. Synthetic biology approaches are also gaining traction, with engineered bacterial cancer therapies in preclinical and clinical trial settings. OUTLOOK A better understanding of the roles of microbes in cancer provides an opportunity to improve each stage of the cancer care cycle, but major challenges remain. Concerted efforts to characterize cancer-associated microbiota among tumor, stool, and blood samples with gold-standard contamination controls would tremendously aid this progress. This would be analogous to The Cancer Genome Atlas’s role in characterizing the cancer somatic mutation landscape. Large-scale clinical trials are currently testing the efficacy of microbiota modulation approaches, ranging from dietary modifications to intratumorally injected, engineered bacteria. These bacterial cancer therapies, if safe and effective, could tremendously expand the cancer therapy armamentarium. Altogether, integrating the host-centric and microbial viewpoints of cancer may improve patient outcomes while providing a nuanced understanding of cancer-host-microbial evolution. Opportunities for microbes to affect cancer care. Diagnosis: Cancer-specific, blood-borne microbial DNA may complement cell-free tumor DNA (ctDNA). Prognosis: Gut and intratumoral microbiota may stratify patient outcomes (NR, nonresponder; R, responder; TME, tumor microenvironment). Therapy: Intratumor injection of CD47 nanobody (CD47nb)–producing Escherichia coli may create systemic antitumor immunity by enhancing dendritic cell (DC) phagocytosis, lymph node (LN) antigen (Ag) presentation, and cytotoxic T lymphocyte (CTL) activity. Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies have provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors in cancer immunotherapy, and engineerable to treat metastases. Despite these findings, the number of microbes known to directly cause carcinogenesis remains small. Critically evaluating and building frameworks for such evidence in light of modern cancer biology is an important task. In this Review, we delineate between causal and complicit roles of microbes in cancer and trace common themes of their influence through the host’s immune system, herein defined as the immuno-oncology-microbiome axis. We further review evidence for intratumoral microbes and approaches that manipulate the host’s gut or tumor microbiome while projecting the next phase of experimental discovery.

C. Malmstrom, Michael D. Martin, L. Gagnevin

Annual Review of Phytopathology • 2022

Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence. Expected final online publication date for the Annual Review of Phytopathology, Volume 60 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

P. Nowicka-Krawczyk, J. Żelazna-Wieczorek, A. Koziróg et al.

Biofouling • 2019

Abstract The scientific multistep approach described herein is a result of two years of research into a control method against microbial fouling and biodeterioration of historic building materials by phototrophs. A series of tests were conducted to select the best antifouling agent for eliminating ‘green’ coatings and protecting surfaces against biofouling. Of the seven active compounds, two with the best penetration abilities were subjected to a photosynthetic activity inhibition test using confocal microscopy. Of the two, a quaternary ammonium salt (QAC) – didecyldimethylammonium chloride (DDAC) – was found to be the most effective. Ten biocides containing QACs at different concentrations were then tested against ‘green’ coatings on wood, brick and plaster, with the best four being selected for further research in model conditions. As a result, biocides containing >14% (v v–1) DDAC were found to be successful antifouling agents for protecting historical materials against biodeterioration by phototrophs.

Magdalena Dyda, Adam Pyzik, E. Wiłkojć et al.

Microorganisms • 2019

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e.g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

Paola Penna, Oscar Stuffer, Alexandra Troi et al.

Applied Mechanics and Materials • 0

<jats:p>What Americas Cup and a heritage building have in common They both aim at innovative technologies and cutting-edge solutions. The owner of the project, an ex-crew member of the most famous sailing match race in the world, pushed the planning team to develop extraordinary solutions for his house. The house, Villa Castelli, is an historical listed building located on the Como lake. During its history, it has been transformed many times, giving as results a non-uniform structure composed by different construction technologies. The aims of the owner were: an overall refurbishment particularly focused on energy efficiency, the exploitation of renewable energy sources based on-site production and a fixed budget. To reach these goals, the energy needs have been reduced improving the performance of the thermal envelope. Then, the building's technical systems have been re-developed in order to exploit as much as possible available renewable energy sources. From the very beginning, it was clear that, for finding optimal solutions, a multidisciplinary approach was necessary. The design approach should be the result of a shared approach integrating different fields, such as creative design, technology, knowledge of material properties, building physics. The great synergy among building envelope retrofitting, innovative technological solutions and the deployment of renewable energy sources allows the transformation of this historical listed building into an outstanding example of a nearly zero energy building (nZEB).</jats:p>

, S. A. Kovalenko, et al.

The Bulletin of Irkutsk State University. Series Biology. Ecology • 2022

<jats:p>Alternative energy and the disposal of pollutants are important areas of development in the field of applied ecology. Microbial fuel cell technology uses pollutants as substrates with a negative energy cost. The electrochemical characteristics of microbial fuel cells (current strength, voltage, power density) were studied to assess the prospects for using Bacillus megaterium MK64-1 (the strain was deposited with VKPM under registration number B-7998) as a bioagent in them. Two nutrient media were used in the experiment – synthetic wastewater and Ashby medium. The volume of the anode chamber of the involved microbial fuel cells is 120 ml, the volume of the cathode chamber is 150 ml. The experiment was set up under aseptic conditions. The total microbial count of the working solution was 4×105 CFU/ml. The experiment included three biological and three analytical replicates. The duration of monitoring the dynamics of fuel cell performance was twelve days. Stabilization of the output voltage was recorded on the fourth day of the experiment. In Ashby medium, starting from the seventh day, electrical indicators continued to grow. The value of external resistance is revealed, at which the highest value of the MFC power is observed - 1 kΩ. The maximum value of the specific power of individual MFC was noted at the level of 14.1 mW/m² in Ashby medium and 13.2 mW/m² in synthetic wastewater. The difference in the composition of nutrient media did not have a significant effect on the dynamics of electrochemical parameters. It is concluded that the studied strain is promising for use in biological fuel cells.</jats:p>

Sahar ELYASİ, Ruşen YAMAÇLI

Cultural Heritage and Science • 0

<jats:p xml:lang="en">Sustainability and cultural heritage are two interconnected and interdependent issues that are essential for achieving sustainable development. Cultural heritage plays a critical role in society as it is an integral part of the social and cultural fabric. This article focuses on the relationship between sustainability and cultural heritage, specifically the integration of cultural heritage into urban and environmentally sustainable development. To achieve this, the study used Tabriz Bazaar as a case study to explore how cultural heritage can be preserved while balancing economic expansion and sustainable development. The research question is how cultural heritage can be integrated into urban and environmentally sustainable development using Tabriz Bazaar as a case study. The hypothesis is that the preservation and protection of cultural heritage values are crucial for achieving sustainable development, and an interdisciplinary approach is necessary to balance economic expansion with cultural heritage preservation. Using a case study approach, the research collected data through a literature review and interviews with experts in the fields of cultural heritage preservation, urban and environmental sustainability, and economics. The research analyzes the challenges of balancing economic development with cultural heritage preservation and proposes an interdisciplinary approach to address these challenges. To make the area more sustainable and preserve its cultural heritage values, specific measures such as promoting cycling in Tabriz Bazaar were recommended. Moreover, education and awareness-raising programs are also necessary to promote the importance of cultural heritage and its contribution to sustainable development. Overall, the research highlights the interdependence between sustainability and cultural heritage and emphasizes the importance of preserving cultural heritage to achieve sustainable development. Policymakers, urban planners, and cultural heritage conservationists can benefit from the findings of this study to develop strategies that promote sustainable development while preserving cultural heritage values.</jats:p>

V. Rótolo, M. Caro, A. Giordano et al.

Flora Mediterranea • 2018

Rotolo, V., De Caro, M. L., Giordano, A. & Palla, F.: Solunto archaeological park in Sicily: life under mosaic tesserae. — Fl. Medit. 28: 233-245. 2018. — ISSN: 1120-4052 printed, 2240-4538 online. Biodeterioration is a complex process induced by the growing and metabolic activity of a wide range of macro and microorganisms, becoming a revelling problem also for the mosaic tesserae of “Casa di Leda” in the Greco - Roman site of Solunto in Sicily. In this case-study, a thick biofilm inducing a deep alteration of mortar and consequently the mosaic tesserae detachment has been highlighted during the restoration plan. The biofilm microbial consortium has been investigated by an integrate approach based on Microscopy analysis (O.M., C.L.S.M.), in vitro culture (Nutrien and Saboraud media) and molecular biology investigation (DNA target sequence amplification, sequencing, sequence analysis). A microbial diversity has been revealed belonging to bacteria ( Bacillus ) and fungi ( Alternaria , Aspergillus ), besides cyanobacteria ( Chroococcus ) and green algae ( Chlorella ). In order to control the biofilm colonization two essential oils (EO), Thymus vulgaris and Origanum vulgare , have been utilized and their antimicrobial activity, preliminarily in vitro (agar disc diffusion methods) and after ex situ and in situ evaluated. This experimentation is aimed at identifying and implementing green biocides for the control of microbial colonization, a promising technology with a reduced impact on human health and environment, able to replace traditional biocide action.

J. Siles, B. Öhlinger, T. Cajthaml et al.

Scientific Reports • 2018

Microbial communities in human-impacted soils of ancient settlements have been proposed to be used as ecofacts (bioindicators) of different ancient anthropogenic activities. In this study, bacterial, archaeal and fungal communities inhabiting soil of three archaic layers, excavated at the archaeological site on Monte Iato (Sicily, Italy) and believed to have been created in a chronological order in archaic times in the context of periodic cultic feasts, were investigated in terms of (i) abundance (phospholipid fatty acid (PLFA) analysis and quantitative PCR)), (ii) carbon(C)-source consumption patterns (Biolog-Ecoplates) and (iii) diversity and community composition (Illumina amplicon sequencing). PLFA analyses demonstrated the existence of living bacteria and fungi in the soil samples of all three layers. The upper layer showed increased levels of organic C, which were not concomitant with an increment in the microbial abundance. In taxonomic terms, the results indicated that bacterial, archaeal and fungal communities were highly diverse, although differences in richness or diversity among the three layers were not detected for any of the communities. However, significantly different microbial C-source utilization patterns and structures of bacterial, archaeal and fungal communities in the three layers confirmed that changing features of soil microbial communities reflect different past human activities.

Xiaoyang Wei, Xue Ling, Liping Yang et al.

Frontiers in Microbiology • 2022

As one of the common physical remains in archaeological discoveries, human bones are important bases for studying the history of human development, which is of great significance for exploring the evolution law of ancient human, reconstructing ancient human society, and tracking the development of human civilization. However, in the process of human bone burial, in addition to being affected by physical and chemical factors, it will also be affected by microorganisms in the buried soil, resulting in a variety of diseases. According to the determination and analysis of the microbial community structure and diversity in the burial soil of Yangguanzhai Site in Gaoling District in Xi’an city, Shaanxi Province, this paper attempts to explore the influence of microorganisms in the burial environment on human bones, in order to provide scientific proof for the microbial prevention and control of bone relics in the archaeological excavation site. For the first time, Illumina NovaSeq high-throughput sequencing technology was used to analyze the microbial community structure in the burial soil. At the phylum level, there were 8 dominant bacteria species in the soil samples of tombs, which were Firmicutes, Actinobacteriota, Actinobacteria, Proteobacteria, Acidobacteriota, Methylomirabilota, Chloroflexi, Bacteroidota. At the genus level, there were 12 dominant species in the soil samples of tombs, including MIZ17, MND1, Gaiella, oc32, Kroppenstedtia, Halomonas, Bacteroides, Dongia, Faecalibacterium, Nocardioides, Pseudomonas, Pseudonocardia. The overall microorganisms in the soil of Yangguanzhai Cemetery were relatively well-distributed, and the microbial community structure near human bones is the most abundant and diverse. Therefore, it is necessary to take some measures to control microorganisms and protect human bones.

Siyu Sun, Zhe Xu, Mengjia Ren et al.

Frontiers in Microbiology • 2024

Introduction The Sanxingdui Site in Guanghan City, Sichuan Province, China, is one of the precious heritage sites of the ancient Chinese civilization. Archaeological work at Sanxingdui is of great significance in clarifying the origins and main contents of the ancient Shu culture and the Yangtze River civilization. Since the 1920s, archaeologists have conducted extensive excavations and research at the site, with particular attention given to the large number of ivory artifacts unearthed. However, the buried ivory is influenced by soil pH, temperature, humidity, and other physical and chemical factors, along with the potential impact of microbial activities that may lead to the corrosion and decomposition of ivory. By understanding the types and activities of microorganisms, appropriate measures can be taken to protect and preserve cultural relics. Methods Multi-point sampling of soil samples around the ivory of the three sacrificial pits at the Sanxingdui site was carried out, and strict aseptic operation was carried out during the sampling process. Subsequently, the microbial community structure and diversity in the buried ivory soil of Sanxingdui site were identified and analyzed by Illumina high-throughput sequencing technology. Results 16S rRNA and internal transcribed spacer sequence analysis revealed significant differences in the soil microbial community structure among different sacrificial pits. The dominant bacterial phyla were the Proteobacteria, GAL15, Actinobacteriota, Bacteroidota, and Methylomirabilota. The dominant fungal phyla were Ascomycota, Mortierellomhcota, and Basidiomycota. Most dominant bacterial and fungal communities play an indispensable role in the ivory corrosion mechanism, promoting the decay and decomposition process through various means such as decomposing organic matter and producing acidic substances. Discussion It is particularly important to take a series of measures to control microbial activity to effectively protect ivory. Our preliminary study of the mechanism of action of microorganisms on ivory in a buried environment provides a scientific basis to prevent and protect against microbial degradation in ancient ivory unearthed in Sanxingdui. Following the research results, suitable antibacterial agents tailored to the preservation environment and microbial characteristics of ancient ivory can be prepared. Ensure that the selected antibacterial agents meet safety and effectiveness requirements to maximize protection against microbial degradation of ancient ivory.

D. De Luca, P. Caputo, Teresa Perfetto et al.

International Journal of Environmental Research and Public Health • 2021

Caves present unique habitats for the development of microbial communities due to their peculiar environmental conditions. In caves decorated with frescoes, the characterization of microbial biofilm is important to better preserve and safeguard such artworks. This study aims to investigate the microbial communities present in the Fornelle Cave (Calvi Risorta, Caserta, Italy) and their correlation with environmental parameters. The cave walls and the wall paintings have been altered by environmental conditions and microbial activity. We first used light microscopy and scanning electron microscopy (SEM) and X-ray diffraction to characterise the biofilm structure and the mineral composition of substrata, respectively. Then, using both culture-dependent (Sanger sequencing) and culture-independent (automated ribosomal intergenic spacer analysis, ARISA) molecular methods, we demonstrated that the taxonomic composition of biofilms was different across the three substrata analysed and, in some cases, positively correlated with some environmental parameters. We identified 47 taxa in the biofilm samples, specifically 8 bacterial, 18 cyanobacterial, 14 algal and 7 fungal taxa. Fungi showed the highest number of ARISA types on the tuff rock, while autotrophic organisms (cyanobacteria and algae) on the frescoes exposed to light. This study confirms that caves constitute a biodiversity-rich environment for microbial taxa and that, in the presence of wall paintings, taxonomic characterization is particularly important for conservation and restoration purposes.

Assefa Getaneh, Tigistu Haile, Luisa Sernicola

Archaeological Prospection • 2018

<jats:title>Abstract</jats:title><jats:p>This geophysical study is part of a multidisciplinary archaeological research project designed to provide the framework for the reconstruction of the cultural and environmental history of the region to the southwest of Aksum and for the production of a detailed archaeological map for the cultural heritage management of central Tigray. Seglamen, near Aksum in north Ethiopia, an area of about 70 000 m<jats:sup>2</jats:sup>, is dated from the early to mid‐first millennium<jats:sc>bce</jats:sc>and has been detected and excavated since 2010 by the Italian Archaeological Expedition of the University of Naples “L'Orientale”. An objective of this study was to develop a geophysical model that defines the archaeological context of a multilayered archaeological site. In doing so, it was also aimed at guiding future excavations operated by archaeologists on the site, thereby assess the geophysical techniques that work well in this area and make recommendations to several archaeological research projects that have been operating at and around Aksum, with similar archaeological context. Magnetic and electrical resistivity tomography (ERT) techniques were employed. The magnetic reconnaissance survey carried out at 2 m station spacing and 5 m line spacing covering the area and has outlined for further detailed investigation localized anomalies for the ERT. Detailed ERT survey was conducted on a rectangular grid of 21.75 × 44.25 m<jats:sup>2</jats:sup>with 0.75 m unit electrode spacing and 0.75 m line spacing. It has yielded two‐dimensional (2D) and three‐dimensional (3D) electrical resistivity sections of the surveyed area. From combined interpretation of the magnetic and electrical imaging survey data, it was possible to delineate localized anomalous zones that could be associated with the existence of subsurface features of archeological interest. Interpreted stone‐based walls were validated through test excavations that revealed well preserved and collapsed walls. These cultural structures are sometimes located at depths of about 20 cm so there is a high possibility of destruction by farming activities of local farmers; ultimately, we would urge conservation work in this area.</jats:p>

Michal Mossberg, S. Vernick, R. Ortenberg et al.

Electroanalysis • 2014

A new method of detecting and diagnosing melanoma based on melanoma biomarker was developed and its feasibility demonstrated. The method is based on an electrochemical biosensor platform comprised of a special biochip and device, performing a multi-channel amperometric detection of the enzymatic activity of tyrosinase, an enzyme biomarker of melanoma. The newly developed biosensor platform is able to electrochemically detect tyrosinase activity in fresh biopsy samples. This bioelectrochemical detection method is rapid, yielding results within minutes from biopsy removal. Using “as is” biopsy samples, without pretreatment, simplifies the process, saves time and reduces cost and labor dramatically. Using modern portable microelectronics provides an accurate biomarker expression measurement at the “point of care” increasing the accessibility of new bio-chip technologies to the public.

Shuiliang Chen, Fangfang Yang, Chungen Li et al.

Journal of Materials Chemistry B • 2015

The electroactive biofilms in the bioelectrodes of traditional bioelectrochemical systems (BES) directly interact with the aqueous solution and usually require a mild aqueous solution environment (e.g. 20 mM acetate and pH = 7.0) to exert their optimum bioelectrocatalytic activity. In this communication, we present a concept of encapsulation of a bioelectrode by a hydrogel for a BES in an alkaline solution environment. A hydrogel-bioelectrode (HBE) was prepared by encapsulating a living electroactive biofilm pre-grown in the bioelectrode with a poly(vinyl alcohol) hydrogel through a freezing/thawing process. Under the protection of the hydrogel, the HBE could keep a high bioelectrocatalytic activity in an alkaline feeding solution with an acetate concentration of over 80 mM and a pH value of 11.0. Moreover it was very stable and tolerated low-frequency ultrasonic vibration. These results imply the extended applications of BESs in the area of high-strength wastewater treatment, portable and implantable devices.

A. Abramson, M. Benami, N. Weisbrod

Environmental Science &amp; Technology • 2013

Enzyme-substrate microbial water tests, originally developed for efficiency gains in laboratory settings, are potentially useful for on-site analysis in remote settings. This is especially relevant in developing countries where water quality is a pressing concern and qualified laboratories are rare. We investigated one such method, Colisure, first for sensitivity to incubation temperatures in order to explore alternative incubation techniques appropriate for remote areas, and then in a remote community of Zambia for detection of total coliforms and Escherichia coli in drinking-water samples. We sampled and analyzed 352 water samples from source, transport containers and point-of-use from 164 random households. Both internal validity (96-100%) and laboratory trials (zero false negatives or positives at incubation between 30 and 40 °C) established reliability under field conditions. We therefore recommend the use of this and other enzyme-based methods for remote applications. We also found that most water samples from wells accessing groundwater were free of E. coli whereas most samples from surface sources were fecally contaminated. We further found very low awareness among the population of the high levels of recontamination in household storage containers, suggesting the need for monitoring and treatment beyond the water source itself.

Y. Hamada, J. Gilbert, Peter E. Larsen et al.

Photogrammetric Engineering &amp; Remote Sensing • 2014

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and below-ground ecosystems. However, the integration of biophysical and soil remote sensing with geospatial information about the environment holds great promise for mapping SMC biogeography. Additional research needs involve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.

Amy V. C. Elliott, L. Warren

Environmental Science &amp; Technology • 2014

Evaluation of lacustrine floc Fe, Pb, and Cd biogeochemistry over seasonal (summer, winter) and water column depth (metalimnetic, hypolimnetic) scales reveals depth-independent seasonally significant differences in floc Fe biominerals and trace element (TE: Pb, Cd) sequestration, driven by floc microbial community shifts. Winter floc [TE] were significantly lower than summer [TE], driven by declining abundance and reactivity of floc amorphous Fe((III))-(oxy)hydroxide (FeOOH) phases under ice ([FeOOH](summer) = 37-77 mgg(-1) vs [FeOOH](winter) = 0.3-7 mgg(-1)). Further, while high summer floc [FeOOH] was observed at both water column depths, winter floc was dominated by Fe((II)) phases. However, the observed seasonal change in the nature and concentrations of floc Fe-phases was independent of water column [Fe], O2, and pH and, instead, significantly correlated to floc bacterial community membership. Bioinformatic modeling (Unifrac, PCA analyses) of in situ and experimental microcosm results identified a temperature-driven seasonal turnover of floc microbial communities, shifting from dominantly putative Fe metabolisms within summer floc to wintertime ancillary Fe reducing and S metabolizing bacteria. This seasonal shift of floc microbial community functioning, significantly the wintertime loss of microbial Fe((II))-oxidizing capability and concomitant increases of sulfur-reducing bacteria, alters dominant floc Fe minerals from Fe((III)) to Fe((II)) phases. This resulted in decreased winter floc [TE], not predicted by water column geochemistry.

Joel Rüthi, Damian Bölsterli, Lucrezia Pardi-Comensoli et al.

Frontiers in Environmental Science • 2020

Plastic pollution poses a threat to terrestrial ecosystems, even impacting soils from remote alpine and arctic areas. Biodegradable plastics are a promising solution to prevent long-term accumulation of plastic litter. However, little is known about the decomposition of biodegradable plastics in soils from alpine and polar ecosystems or the microorganisms involved in the process. Plastics in aquatic environments have previously been shown to form a microbial community on the surface of the plastic distinct from that in the surrounding water, constituting the so-called “plastisphere.” Comparable studies in terrestrial environments are scarce. Here, we aimed to characterize the plastisphere microbiome of three types of plastics differing in their biodegradability in soil using DNA metabarcoding. Polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), and polyethylene (PE) were buried in two different soils, from the Swiss Alps and from Northern Greenland, at 15°C for 8 weeks. While physico-chemical characteristics of the polymers only showed minor (PLA, PBAT) or no (PE) changes after incubation, a considerably lower α-diversity was observed on the plastic surfaces and prominent shifts occurred in the bacterial and fungal community structures between the plastisphere and the adjacent bulk soil not affected by the plastic. Effects on the plastisphere microbiome increased with greater biodegradability of the plastics, from PE to PLA. Copiotrophic taxa within the phyla Proteobacteria and Actinobacteria benefitted the most from plastic input. Especially taxa with a known potential to degrade xenobiotics, including Burkholderiales, Caulobacterales, Pseudomonas, Rhodococcus, and Streptomyces, thrived in the plastisphere of the Alpine and Arctic soils. In addition, Saccharimonadales (superphylum Patescibacteria) was identified as a key taxon associated with PLA. The association of Saccharibacteria with plastic has not been reported before, and pursuing this finding further may shed light on the lifestyle of this obscure candidate phylum. Plastic addition affected fungal taxa to a lesser extent since only few fungal genera such as Phlebia and Alternaria were increased on the plastisphere. Our findings suggest that the soil microbiome can be strongly influenced by plastic pollution in terrestrial cryoenvironments. Further research is required to fully understand microbial colonization on plastic surfaces and the biodegradation of plastic in soils.

Peter E. Larsen, Nicole Scott, A. Post et al.

The ISME Journal • 2014

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.

Sujata Dey, A. K. Rout, B. Behera et al.

Environmental Microbiome • 2022

It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ‘‘plastisphere”. The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz . autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Elena Quintanilla, C. Rodrigues, I. Henriques et al.

Frontiers in Microbiology • 2022

Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals’ taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.

U. Karaoz, Eoin L. Brodie

Frontiers in Bioinformatics • 2022

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.

J. Zorz, Carmen Li, Anirban Chakraborty et al.

ISME Communications • 2023

Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson’s r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.

Nicholas Bock, F. Van Wambeke, M. Dion et al.

Biogeosciences • 2018

Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

D. Lipus, A. Vikram, R. Hammack et al.

Geomicrobiology Journal • 2019

Abstract The petroleum industry has an increasing interest in understanding the microbial communities driving biofouling and biocorrosion in reservoirs, wells, and infrastructure. However, sampling of the relevant produced fluids from subsurface environments for microbiological analyses is often challenged by high liquid pressures, workplace regulations, operator liability concerns, and remote sampling locations. These challenges result in infrequent sampling opportunities and the need to store and preserve the collected samples for several days or weeks. Maintaining a representative microbial community structure from produced fluid samples throughout storage and handling is essential for accurate results of downstream microbial analyses. Currently, no sample handling or storage recommendations exist for microbiological analyses of produced fluid samples. We used 16S rRNA gene sequencing to monitor the changes in microbial communities in hypersaline produced water stored at room temperature or at 4 °C for up to 7 days. We also analyzed storage at −80 °C across a 3-week period. The results suggest ideal handling methods would include placing the collected sample on ice as soon as possible, but at least within 24 h, followed by shipping the samples on ice over 2–3 days, and finally, long-term storage in the −20 °C or −80 °C freezer.

Katja Metfies, J. Hessel, Robin Klenk et al.

PLOS ONE • 2020

In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak of Miracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.

Vilma Pérez, Johanna Cortés, F. Marchant et al.

Microorganisms • 2020

Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42–72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.

M. Pavlovska, I. Prekrasna, I. Parnikoza et al.

Microbes and Environments • 2021

Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.

Catherine Marois, C. Girard, Y. Klanten et al.

Frontiers in Microbiology • 2022

Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.

M. Papale, Gabriella Caruso, G. Maimone et al.

Water • 2023

Polar marine environments host a complex assemblage of cold-adapted auto- and heterotrophic microorganisms that affect water biogeochemistry and ecosystem functions. However, due to logistical difficulties, remote regions like those in close proximity to glaciers have received little attention, resulting in a paucity of microbiological data. To fill these gaps and obtain novel insights into microbial structure and function in Arctic regions, a survey of microbial communities in an area close to the Blomstrandbreen glacier in Kongsfjorden (Svalbard Archipelago; Arctic Ocean) was carried out during an early summer period. An Unmanned Autonomous Vehicle designed to safely obtain seawater samples from offshore-glacier transects (PROTEUS, Portable RObotic Technology for Unmanned Surveys) was equipped with an automatic remotely-controlled water multi-sampler so that it could sample just beneath the glacier, where access from the sea is difficult and dangerous. The samples were analysed by image analysis for the abundance of total prokaryotes, viable and respiring cells, their morphological traits and biomass; by flow cytometry for autotrophic and prokaryotic cells (with high and low nucleic acid contents) as well as virus-like particle counts; by BIOLOG ECOPLATES for potential community metabolism; and by fluorimetry for potential enzymatic activity rates on organic polymers. Contextually, the main physical and chemical (temperature, salinity, pH, dissolved oxygen and nutrients) parameters were detected. Altogether, besides the PROTEUS vehicle’s suitability for collecting samples from otherwise inaccessible sites, the multivariate analysis of the overall dataset allowed the identification of three main sub-regions differently affected by the haline gradient (close to the glacier) or terrigenous inputs coming from the coast. A complex microbiological scenario was depicted by different patterns of microbial abundance and metabolism among the transects, suggesting that ice melting and Atlantic water inflow differently supported microbial growth.

Emily Smenderovac, Caroline E. Emilson, Karelle Rheault et al.

Scientific Reports • 2024

Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at − 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at − 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.

xiaoqian gu, Zhe Cao, Luying Zhao et al.

International Journal of Molecular Sciences • 2023

Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.

Nanxi Lu, Alicia Sanchez-Gorostiaga, Mikhail Tikhonov et al.

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<jats:title>Abstract</jats:title><jats:p>Microbial invasions exhibit many unique properties; notably, entire microbial communities often invade one another, a phenomenon known as community coalescence. In spite of the potential importance of this process for the dynamics and stability of microbiome assembly, our understanding of it is still very limited. Recent theoretical and empirical work has proposed that large microbial communities may exhibit an emergent cohesiveness, as a result of collective consumer-resource interactions and metabolic feedbacks between microbial growth and the environment. A fundamental prediction of this proposal is the presence of ecological co-selection during community coalescence, where the invasion success of a given taxon is determined by its community members. To establish the generality of this prediction in experimental microbiomes, we have performed over one hundred invasion and coalescence experiments with environmental communities of different origins that had spontaneously and stably assembled in two different synthetic aerobic environments. We show that the dominant species of the coalesced communities can both recruit their community members (top-down co-selection) and be recruited by them (bottom-up co-selection) into the coalesced communities. Our results provide direct evidence that collective invasions generically produce ecological co-selection of interacting species, emphasizing the importance of community-level interactions during microbial community assembly.</jats:p>

Emily B. Graham, James C. Stegen

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<jats:title>Abstract</jats:title><jats:p>Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative influence of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function, which we define generically to represent any biogeochemical reaction of interest. We used an ecological simulation model to evaluate this hypothesis. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by deterministic selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal rates high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer its biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.</jats:p>

M. Gebreslassie, C. Cuvilas, Collen Zalengera et al.

Energy, Sustainability and Society • 2022

Background Off-grid and decentralized energy systems have emerged as an alternative to facilitate energy access and resilience in a flexible, adaptable way, particularly for communities that do not have reliable access to centralized energy networks both in rural and urban areas. Much research to date on community energy systems has focused on their deployment in Europe and North America. This paper advances these debates by looking at how community energy systems can support energy transitions in Africa. Specifically, it asks: what role can community energy systems play in the energy transition in East and Southern Africa? Results This article investigates the potential for community energy to foster sustainable and just energy transitions in two countries in East and Southern Africa, namely Ethiopia and Mozambique. To do so, it explores transformations in Ethiopia and Mozambique’s energy systems through the lens of energy landscapes. This concept enables us to situate energy transitions within recent developments in energy governance and to understand current and future possibilities for change through the involvement of communities that currently lack access to reliable and clean energy. Our results show that when countries face the prospects of lucrative energy investments in natural gas or large hydropower, renewables are often deprioritized. Their suitability to address energy challenges and access gaps is de-emphasized, even though there is little evidence that investment in large-scale generation can handle the energy needs of the most disadvantaged groups. Initiatives and policies supporting community-focused renewable energy have remained limited in both countries. They tend to be designed from the top-down and focused on rural areas when they exist. Conclusions Energy transitions in Ethiopia and Mozambique, and many other countries with significant gaps in access to centralized energy systems, require putting inclusivity at the forefront to ensure that energy policies and infrastructure support the well-being of society as a whole. As long as investments in off-grid energy continue to depend on international organizations’ goodwill or development aid programs outside the ambit of national energy plans, energy access gaps will remain unaddressed, and there will not be a genuine and just transition to sustainable energy.

M. Mohseni, S. F. Moosavian, A. Hajinezhad

Energy Science &amp; Engineering • 2022

Off‐grid renewable energy systems are a solution for power generation in areas where access to the grid is not possible or cost‐effective; in particular, low population rural areas located far away from grid lines or in rugged terrains. Furthermore, over‐reliance on fossil fuels for supplying global energy demand has led to the depletion of nonrenewable resources and environmental issues. This paper presents a feasibility assessment of an off‐grid hybrid renewable energy system for a remote rural area in Kohgiluye and Boyer‐Ahmad Province in Iran. Regarding the available energy resources in the region, a photovoltaic (PV)‐biomass energy system is considered. HOMER Pro software is utilized to find the optimized sizing of the PV‐biomass system to fulfill this load demand. The objective function in this optimization is the system's total net present cost. Due to the rapid fluctuation of economic factors in the country, several rates of inflation and discount rate are considered to investigate their influence on the costs of the system. The optimization result for the current inflation rate of 40% and the discount rate of 18% in the country proposes a hybrid energy system consisting of a 3 kW biogas‐fueled generator, 4.74 kW PV, 10 kWh battery, and 2.07 kW converter to meet the 2.64 kW peak load and 14.53 kWh/day consumption of the community. The total net present cost and cost of energy are $93,057 and 0.0933 $/kWh, respectively. Finally, the environmental assessment of the proposed hybrid system shows an annual CO2 emission of 2.95 kg, which means 99.9% CO2 emissions mitigation compared to a conventional coal‐based electrical plant.