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Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Gut microbiome dysbiosis is linked to many neurological disorders including Alzheimer's disease (AD). A major risk factor for AD is polymorphism in the apolipoprotein E ( APOE ) gene, which affects gut microbiome composition. To explore the gut-brain axis in AD, long-lived animal models of naturally developing AD-like pathologies are needed. Octodon degus (degu) exhibit spontaneous AD-like symptoms and ApoE mutations, making them suitable for studying the interplay between AD genetic determinants and gut microbiome. We analyzed the association between APOE genotype and gut microbiome in 50 humans and 32 degu using16S rRNA gene amplicon sequencing. Significant associations were found between the degu ApoE mutation and gut microbial changes in degu, notably a depletion of Ruminococcaceae and Akkermansiaceae and an enrichment of Prevotellaceae , mirroring patterns seen in people with AD. The altered taxa were previously suggested to be involved in AD, validating the degu as an unconventional model for studying the AD/microbiome crosstalk., Competing Interests: The authors declare no competing interests., (© 2024 The Authors.)

Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio , harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer . The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio , exhibiting patterns that mirror the host phylogeny., Importance: Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer 's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment., Competing Interests: The authors declare no conflict of interest.

Although the Antarctic lakes are of great importance for the climate and the carbon cycle, the lithological influences on the input of elements that are necessary for phytoplankton in lakes have so far been insufficiently investigated. To address this issue, we analyzed phytoplankton cell concentrations and chemical compositions of water samples from lakes, ponds and a stream on Fildes and Ardley Islands of King George Island in the South Shetland Archipelago. Furthermore, lake sediments, as well as soil and rock samples collected from the littoral zone were analyzed for their mineralogical/petrographic composition and pollutant contents of polycyclic aromatic hydrocarbons (PAHs). In addition, leaching experiments were carried out to with the lithologic samples to investigate the possible changes in pH, alkalinity, macronutrients (N, P, Si), micronutrients (e.g. Fe, Zn, Cu, Mn), anions (S, F, Br), and other cations (e.g. Na, K, Mg, Ca, Al, Ti, V, Cr, Co, Ni, As, Se, Pb, Sb, Mo, Ag, Cd, Sn, Ba, Tl, B). Our results showed that phytoplankton levels varied between 15 and 206 cells/mL. Chlorophyll-a concentrations showed high correlations with NH 4 , NO 3 . The low levels of PO 4 (<0.001 mg/L) indicated a possible P-limitation in the studied lakes. The composition of rock samples ranged from basalt to trachybasalt with variable major oxide (e.g. SiO 2 , Na 2 O and K 2 O) contents and consist mainly quartz, albite, calcite, dolomite and zeolite minerals. The concentrations of total PAHs were below the toxic threshold levels (9.55-131.25 ng g -1 dw). Leaching experiments with lithologic samples indicated major increase in pH (up to 9.77 ± 0.02) and nutrients, especially PO 4 (1.03 ± 0.04 mg/L), indicating a strong P-fertilization impact in increased melting scenarios. Whereas, toxic elements such as Pb, Cu, Cd, Al and As were also released from the lithology, which may reduce the phytoplankton growth., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: N. Olgun reports financial support was provided by Technological Research Council of Türkiye. N. Olgun reports a relationship with Technological Research Council of Türkiye that includes: funding grants., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets., (© 2023 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)

Marine free-living (FL) and plankton-associated prokaryotes (plankton-microbiota) are at the basis of trophic webs and play crucial roles in the transfer and cycling of nutrients, organic matter, and contaminants. Different ecological niches exist along the plankton size fraction gradient. Despite its relevant ecological role, the plankton-microbiota has rarely been investigated with a sufficient level of size-fraction resolution, and it can be challenging to study because of overwhelming eukaryotic DNA. Here we compared the prokaryotic diversity obtained by 16S rRNA gene sequencing from six plankton size fractions (from FL to mesoplankton), through three DNA recovery methods: direct extraction, desorption pretreatment, enrichment post-treatment. The plankton microbiota differed strongly according to the plankton size-fraction and methodological approach. Prokaryotic taxa specific to each size fraction, and methodology used, were identified. Vibrionaceae were over-represented by cell desorption pretreatment, while prokaryotic DNA enrichment had taxon-specific effects, indicating that direct DNA extraction was the most appropriate method., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying ( hgc + ) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc + microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales , hgc + microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales , Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying ( hgc + ) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc + microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales , Phycisphaerae , and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater., Competing Interests: The authors declare no conflict of interest.

This paper looks at experiential feedback and the technical and scientific challenges tied to the MERITE-HIPPOCAMPE cruise that took place in the Mediterranean Sea in spring 2019. This cruise proposes an innovative approach to investigate the accumulation and transfer of inorganic and organic contaminants within the planktonic food webs. We present detailed information on how the cruise worked, including 1) the cruise track and sampling stations, 2) the overall strategy, based mainly on the collection of plankton, suspended particles and water at the deep chlorophyll maximum, and the separation of these particles and planktonic organisms into various size fractions, as well as the collection of atmospheric deposition, 3) the operations performed and material used at each station, and 4) the sequence of operations and main parameters analysed. The paper also provides the main environmental conditions that were prevailing during the campaign. Lastly, we present the types of articles produced based on work completed by the cruise that are part of this special issue., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Freshwater ecosystems are important contributors to the global greenhouse gas budget and a comprehensive assessment of their role in the context of global warming is essential. Despite many reports on freshwater ecosystems, relatively little attention has been given so far to those located in the southern hemisphere and our current knowledge is particularly poor regarding the methane cycle in non-perennially glaciated lakes of the maritime Antarctica. We conducted a high-resolution study of the methane and carbon dioxide cycle in a lake of the Fildes Peninsula, King George Island (Lat. 62°S), and a succinct characterization of 10 additional lakes and ponds of the region. The study, done during the ice-free and the ice-seasons, included methane and carbon dioxide exchanges with the atmosphere (both from water and surrounding soils) and the dissolved concentration of these two gases throughout the water column. This characterization was complemented with an ex-situ analysis of the microbial activities involved in the methane cycle, including methanotrophic and methanogenic activities as well as the methane-related marker gene abundance, in water, sediments and surrounding soils. The results showed that, over an annual cycle, the freshwater ecosystems of the region are dominantly autotrophic and that, despite low but omnipresent atmospheric methane emissions, they act as greenhouse gas sinks., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

High latitudes are experiencing intense ecosystem changes with climate warming. The underlying methane (CH 4 ) cycling dynamics remain unresolved, despite its crucial climatic feedback. Atmospheric CH 4 emissions are heterogeneous, resulting from local geochemical drivers, global climatic factors, and microbial production/consumption balance. Holistic studies are mandatory to capture CH 4 cycling complexity. Here, we report a large set of integrated microbial and biogeochemical data from 387 samples, using a concerted sampling strategy and experimental protocols. The study followed international standards to ensure inter-comparisons of data amongst three high-latitude regions: Alaska, Siberia, and Patagonia. The dataset encompasses different representative environmental features (e.g. lake, wetland, tundra, forest soil) of these high-latitude sites and their respective heterogeneity (e.g. characteristic microtopographic patterns). The data included physicochemical parameters, greenhouse gas concentrations and emissions, organic matter characterization, trace elements and nutrients, isotopes, microbial quantification and composition. This dataset addresses the need for a robust physicochemical framework to conduct and contextualize future research on the interactions between climate change, biogeochemical cycles and microbial communities at high-latitudes., (© 2022. The Author(s).)

During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH 4 + ) is released by amino acid degradation. High NH 4 + concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH 4 + and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH 4 + acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH 4 + inputs of increasing intensity (from 1.7 to 15.2 g N-NH 4 + liters -1 ) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH 4 + gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus . Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium ) and syntrophic VFA oxidizers (mainly Syntrophaceticus ) with increasing NH 4 + concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium , Sporanaerobacter , Terrisporobacter ) and syntrophic VFA oxidizers (mainly Tepidanaerobacter , Syntrophomonas ). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH 4 + tolerance capacity among VFA producers and syntrophic VFA oxidizers.

Freshwater ecosystems are responsible for an important part of the methane (CH 4 ) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH 4 flux measurements, CH 4 production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H 2 /CO 2 , resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H 2 /CO 2 -derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H 2 /CO 2 (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H 2 /CO 2 -based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H 2 -production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Schwob, Segovia, González-Wevar, Cabrol, Orlando and Poulin.)

Lentic ecosystems play a major role in the global carbon cycling but the understanding of the environmental determinants of lake metabolism is still limited, notably in small artificial lakes. Here the effects of environmental conditions on lake metabolism and CO 2 and CH 4 emissions were quantified in 11 small artificial gravel pit lakes covering a gradient of ecosystem maturity, ranging from young oligotrophic to older, hypereutrophic lakes. The diffusive fluxes of CO 2 and CH 4 ranged from -30.10 to 37.78 mmol m -2 d -1 and from 3.05 to 25.45 mmol m -2 d -1 across gravel pit lakes, respectively. Nutrients and chlorophyll a concentrations were negatively correlated with CO 2 concentrations and emissions but positively correlated with CH 4 concentrations and emissions from lakes. These findings indicate that, as they mature, gravel pit lakes switch from heterotrophic to autotrophic-based metabolism and hence turn into CO 2 -sinks. In contrast, the emission of CH 4 increased along the maturity gradient. As a result, eutrophication occurring during ecosystem maturity increased net emissions in terms of climate impact (CO 2 equivalent ) due to the higher contribution of CH 4 emissions. Overall, mean CO 2equivalent emission was 7.9 g m -2 d -1 , a value 3.7 and 4.7 times higher than values previously reported in temperate lakes and reservoirs, respectively. While previous studies reported that lakes represent emitters of C to the atmosphere, this study highlights that eutrophication may reverse lake contribution to global C budgets. However, this finding is to be balanced with the fact that eutrophication also increased CH 4 emissions and hence, enhanced the potential impact of these ecosystems on climate. Implementing mitigation strategies for maintaining intermediate levels of maturity is therefore needed to limit the impacts of small artificial waterbodies on climate. This could be facilitated by their small size and should be planned at the earliest stages of artificial lake construction., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Arctic lakes emit methane (CH 4 ) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH 4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH 4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH 4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH 4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH 4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH 4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH 4 cycle in lakes, a crucial component of the global CH 4 cycle., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia , were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed., (Copyright © 2020 Schwob, Cabrol, Poulin and Orlando.)

It is commonly assumed that methane (CH 4 ) released by lakes into the atmosphere is mainly produced in anoxic sediment and transported by diffusion or ebullition through the water column to the surface of the lake. In contrast to that prevailing idea, it has been gradually established that the epilimnetic CH 4 does not originate exclusively from sediments but is also locally produced or laterally transported from the littoral zone. Therefore, CH 4 cycling in the epilimnion and the hypolimnion might not be as closely linked as previously thought. We utilized a high-resolution method used to determine dissolved CH 4 concentration to analyze a Siberian lake in which epilimnetic and hypolimnetic CH 4 cycles were fully segregated by a section of the water column where CH 4 was not detected. This layer, with no detected CH 4 , was well below the oxycline and the photic zone and thus assumed to be anaerobic. However, on the basis of a diffusion-reaction model, molecular biology, and stable isotope analyses, we determined that this layer takes up all the CH 4 produced in the sediments and the deepest section of the hypolimnion. We concluded that there was no CH 4 exchange between the hypolimnion (dominated by methanotrophy and methanogenesis) and the epilimnion (dominated by methane lateral transport and/or oxic production), resulting in a vertically segregated lake internal CH 4 cycle.

The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L -1 ). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L -1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2-3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum Bacteroidetes . Members of the order Saprospirales were enriched from sediment in natural seawater (initial pH > 8), while the family Flavobacteriaceae was favored by acidified seawater (initial pH < 8). Some Flavobacteriaceae members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems.

One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service. The analysis of microbial community revealed a wide phylogenetic diversity that contributes in different-and still mostly unclear-ways to hydrogen production. Bridging this gap of knowledge between microbial ecology features and ecosystem functionality is essential to optimize the bioprocess and develop strategies toward a maximization of the efficiency and stability of substrate conversion. The aim of this review is to provide a comprehensive overview of the most up-to-date biodata available and discuss the main microbial community features of biohydrogen engineered ecosystems, with a special emphasis on the crucial role of interactions and the relationships between species composition and ecosystem service. The elucidation of intricate relationships between community structure and ecosystem function would make possible to drive ecosystems toward an improved functionality on the basis of microbial ecology principles., (© FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Sodium azide (NaN 3 ) was evaluated as inhibitor of microbial growth and activity in marine sediment resuspensions by monitoring the abundance of free-living and sessile bacteria using both flow cytometry and qPCR methods. Results show that 50mM of NaN 3 strongly inhibits bacterial growth under natural and enriched resource conditions., (Copyright © 2016 Elsevier B.V. All rights reserved.)

To provide new insight into the dark fermentation process, a multi-lateral study was performed to study the microbiology of 20 different lab-scale bioreactors operated in four different countries (Brazil, Chile, Mexico, and Uruguay). Samples (29) were collected from bioreactors with different configurations, operation conditions, and performances. The microbial communities were analyzed using 16S rRNA genes 454 pyrosequencing. The results showed notably uneven communities with a high predominance of a particular genus. The phylum Firmicutes predominated in most of the samples, but the phyla Thermotogae or Proteobacteria dominated in a few samples. Genera from three physiological groups were detected: high-yield hydrogen producers (Clostridium, Kosmotoga, Enterobacter), fermenters with low-hydrogen yield (mostly from Veillonelaceae), and competitors (Lactobacillus). Inocula, reactor configurations, and substrates influence the microbial communities. This is the first joint effort that evaluates hydrogen-producing reactors and operational conditions from different countries and contributes to understand the dark fermentation process.

Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.

The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD.

To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester.

Molecular biology techniques provide valuable insights in the investigation of microbial dynamics and evolution. Denaturing gradient gel electrophoresis (DGGE) analysis is one of the most popular methods which have been used in bioprocess assessment. Most of the anaerobic digestion models consider several microbial populations as state variables. However, the difficulty of measuring individual species concentrations may cause inaccurate model predictions. The integration of microbial data and ecosystem modelling is currently a challenging issue for improved system control. A novel procedure that combines common experimental measurements, DGGE, and image analysis is presented in this study in order to provide a preliminary estimation of the actual concentration of the dominant bacterial ribotypes in a bioreactor, for further use as a variable in mathematical modelling of the bioprocess. This approach was applied during the start-up of a continuous anaerobic bioreactor for hydrogen production. The experimental concentration data were used for determining the kinetic parameters of each species, by using a multi-species chemostat-model. The model was able to reproduce the global trend of substrate and biomass concentrations during the reactor start-up, and predicted in an acceptable way the evolution of each ribotype concentration, depicting properly specific ribotype selection and extinction.

Since full-scale biofilters are often operated under fluctuating conditions, it is critical to understand their response to transient states. Four pilot-scale biofilters treating a composting gas mixture and undergoing repeated substrate pulses of increasing intensity were studied. A systematic approach was proposed to quantify the resistance and resilience capacity of their removal efficiency, which enabled to distinguish between recalcitrant (ammonia, DMDS, ketones) and easily degradable (esters and aldehyde) compounds. The threshold of disturbing shock intensity and the influence of disturbance history depended on the contaminant considered. The spatial and temporal distribution of the bacterial community structure in response to the perturbation regime was analysed by Denaturing Gradient Gel Electrophoresis (DGGE). Even if the substrate-pulses acted as a driving force for some community characteristics (community stratification), the structure-function relationships were trickier to evidence: the distributions of resistance and composition were only partially coupled, with contradictory results depending on the contaminant considered., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.

In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.

Background: "Dialysis dose," a concept developed by Sargent and Gotch based on urea kinetic modeling, is a useful and recognized tool that is used to quantitate and optimize a dialysis-efficacy program. However, it has been shown that oversimplification of the "dialysis adequacy" concept to the Kt/V index might lead to dramatic underdialysis and subsequent deleterious consequences on morbidity and mortality of dialysis patients. With this perspective, the determination of Kt/V must be very cautious and rely on accurate measurement of postdialysis urea concentration and its use integrated as a tool in a quality-assurance process., Methods: In this study, we analyzed urea dynamics by means of a blood side (ultrafiltrate) continuous online urea monitoring system interfaced with a two-pool model hosted in a microcomputer. The study was designed to provide instantaneous dialysis performances (body and dialyzer clearances, dialyzer mass transfer coefficient) and to determine the in vivo functional permeability characteristics of the patient [intercompartment urea mass transfer coefficient (Kc)]. Thirteen end-stage renal disease patients (age 54 +/- 16 years; 12 male and 1 female) were studied during nine consecutive dialysis sessions (3 weeks)., Results: Urea kinetics obtained from the urea monitoring system fitted closely the urea kinetic modeling prediction, confirming the validity of the double-pool model structure. Effective in vivo urea mass transfer coefficient averaged 912 +/- 235 mL/min/1.73 m2, a value close to those reported with more invasive methods. Large variations ranging from 363 to 1249 mL/min were observed among patients, confirming very large interindividual patient permeability differences. Interestingly, the urea mass transfer coefficient was inversely correlated with the postdialysis rebound values. Intraindividual variations were also noted as a function of time denoting functional changes in urea mass transfer coefficient values. The urea distribution volume was 38.1 +/- 7, 8 L (53 +/- 8% body weight). V1 referring to the extracellular volume and V2 to the intracellular volume were 9 +/- 2 L (13 +/- 2% body weight) and 29.2 +/- 6.6 L (41 +/- 1.3% body wt), respectively. The extracellular/intracellular volume ratio was 0.31 (approximately one third) and was not as usually defined by the paradigm 1/2 ratio., Conclusion: Online double-pool urea kinetic modeling gave a new insight in urea kinetic modeling approach. Urea dynamics fit perfectly a double-compartment model structure. Accessible extracellular volume to hemodialysis is smaller than expected. The in vivo urea mass transfer coefficient must be considered as an individual and variable characteristic of ESRD patients that should be taken into consideration when prescribing the hemodialysis schedule.