Benthic Microbial Communities Research Articles

Response of Microbial Communities to Naturally Occurring Radioactive Material-Contaminated Sediments: A Microcosm-Based Study.

There is a growing need to understand the potential ecological impacts of contaminants in offshore oil and gas infrastructure, especially if that infrastructure is to be left in situ as a decommissioning option. Naturally occurring radioactive material (NORM) is one type of contaminant found in solid deposits on internal surfaces of infrastructure that poses potential ecological harm if released into the marine environment. Microbes are important components of marine sediment ecosystems because they provide ecosystem services, yet the impacts of NORM contamination to these communities are not well understood. The present study aimed to investigate the response of benthic microbial communities to NORM-contaminated scale, collected from an offshore oil and gas system, via controlled laboratory microcosm studies. Changes to microbial communities in natural sediment and sediments spiked with NORM at radium-226 activity concentrations ranging from 9.5 to 59.8 Bq/kg (in partial equilibria with progeny) over 7 and 28 days were investigated using high-throughput sequencing of environmental DNA extracted from experimental sediments. There were no significant differences in microbial community composition between control and scale-spiked sediments over 7 and 28 days. However, we observed a greater presence of Firmicutes in the scale-mixed treatment and Chloroflexi in the scale-surface treatments after 28 days. This could suggest selection for species with contaminant tolerance or potential resilience to radiation and metal toxicity. Further research is needed to explore microbial tolerance mechanisms and their potential as indicators of effects of radionuclide-contaminated sediments. The present study demonstrated that microcosm studies can provide valuable insights about the potential impacts of contamination from oil and gas infrastructure to sediment microbial communities. Environ Toxicol Chem 2024;43:1648-1661. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

High potential in synergizing the reduction of dissolved organic carbon concentration and carbon dioxide emissions for submerged-vegetation-covered river networks

Various technologies and projects have been explored and developed for the synergetic control of environmental pollution and carbon emissions in aquatic ecosystems. Planting submerged vegetation in shallow waters was also expected to achieve this purpose. However, the magnitude and mechanism of carbon dioxide (CO2) emission affected by submerged vegetation is not clear enough in complex aquatic ecosystems. This study investigated the influences of submerged plants on CO2 emission, ecosystem metabolism features, and microbial community traits based on observations in river networks on the Changjiang River Delta. The results showed that CO2 emission from planted waters accounted for 73% of unplanted waters. Meanwhile, planted waters had higher dissolved organic carbon removal capacity in overlying water and higher potential of carbon sequestration in sediment at the same time. These distinctions between the two habitats were attributed to (1) improved CO2 and bicarbonate consumption in water columns via enhancing photosynthesis and (2) inhibited CO2 production by reconstructing the benthic microbial community. Additional eco-advantages were found in planted sediments, such as a high potential of methane oxidation and xenobiotics biodegradation and a low risk of becoming black and odorous. In brief, submerged vegetation is beneficial in promoting pollution removal and carbon retention synchronously. This study advances our understanding of the feedback between aquatic metabolism and CO2 emission.

Contrasting benthic bacterial and fungal communities in two temperate coastal areas affected by different levels of anthropogenic pressure

Benthic microbial communities play a crucial role in maintaining the stability and function of estuarine ecosystems. However, their organization and response to multiple stresses in severely disturbed coastal areas remains to be elucidated. In this study, we revealed the presence of contrasting benthic bacterial and fungal communities in the Liaohe (LH) and Yalujiang (YLJ) estuaries, which are located at similar latitudes and are characterized by similar climates but are subjected to different levels of anthropogenic pressure. The results showed that Firmicutes and Chloroflexi were more abundant in LH, which reflected the influence of anthropogenic pressure in this area. Functional analyses indicated that the functional genes involved in the generation of precursor metabolites and energy pathways were more enriched in the LH community, while genes regulating degradation/utilization/assimilation processes were more enriched in the YLJ community. Distance-dependent similarity analysis showed that the bacterial community in LH was more affected by environmental changes, while that in YLJ was more influenced by geographic dispersion. In contrast, no significant distance-dependent similarity was found for the fungal communities in the two areas. In addition, the network analysis showed that the bacterial-fungal network in YLJ was more complex and stable than that in the LH. Our results highlight the important roles of environmental heterogeneity in controlling microbial community composition, biogeographic patterns, and co-occurrence networks. These findings fill knowledge gaps in the understanding of the different response patterns of benthic communities under varying anthropogenic pressures.

Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming.

Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then used to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.

Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea.

The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.

Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan.

Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.

Metagenomic probing toward an atlas of the taxonomic and metabolic foundations of the global ocean genome

The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science and society with a growing range of biotechnology applications in sectors such as biomedicine, energy, and food. Shotgun sequencing and metagenomics can now be used to catalog the diversity of ocean microbial life and to explore its functional potential, but has been limited by sample coverage, access to suitable sequencing platforms, and computational capacity. Here we provide a novel synthesis of the global ocean genome based on analysis of 2,102 sampled ocean metagenomes, with gene assembly and annotation via the KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing 308.6 million gene clusters. Taxonomically, we report the distribution of marine genes across the tree of life and different ocean basins and depth zone biomes. Functionally, we map its relationship to protein families and biogeochemical processes, including the major microbial metabolic pathways that process three elements that play fundamental roles in biogeochemical cycles and are relevant to climate change. These data extend our understanding of the complex, dynamic nature of the ocean microbiome and its metabolic capabilities. Further research is of critical global importance both to unlock the potential of the ocean genome and to understand and predict the effects of human-induced changes, including pollution and climate change. Further hypothesis-driven research should target under-sampled deep sea and benthic microbial communities using enhanced metagenomic methods, to better understand marine ecosystem functioning. Investment in the necessary computational capacity is essential, as are suitable intellectual property frameworks.

The impact of mariculture biofilters on the distribution of benthic nutrient fluxes, organic matters and bacterial community in a mariculture wastewater treatment system

Constructed-wetlands, biofilms, and sedimentation are among biological filters used in mariculture wastewater treatments, however, their impacts on the distribution of benthic microbial community and inorganic-nutrient fluxes have not been fully explored. This study applied 16 S rRNA high-throughput sequencing technology to investigate the microbial community distribution and their impacts on nutrient fluxes in mariculture biofilters system. Results showed that bacterial community compositions were significantly different in the constructed-wetland and biofilm treatments (p < 0.05) relative to sedimentation. The composition of the 16 S rRNA genes among the treatments were enriched with Proteobacteria (73%), Bacteroidetes (69%), Firmicutes (62%), and Flavobacteria (61%) in Biofilm compared to Proteobacteria (53%), Bacteroidetes (39%), Firmicutes (32%), and Flavobacteria (21%) in constructed wetlands. NMDS analysis showed that bacterial composition in constructed-wetland and biofilms clustered separately compared to sedimentation treatment. Functional-Annotation-of-Prokaryotic-Taxa analysis indicated that the proportions of sediment-microbial-functional groups (aerobic-chemoheterotrophy, chemoheterotrophy, and nitrate-ammonification) were 47% in the constructed-wetland, 32% in biofilm and 13% in sedimentation system. Benthic-nutrient fluxes for phosphate, ammonium, nitrite, nitrate and sediment oxygen consumption differed markedly among the treatments (p < 0.05). Canonical correspondence analysis indicated constructed-wetland had the strongest association between biogeochemical contents and the bacterial community relative to other treatments. This study suggests that the mariculture wastewater biofilters promoted microbial community distributions, sediment bacterial functional-groups including chemoheterotrophy, aerobic-chemoheterotrophy, denitrification, and nitrification and interactions with nutrient fluxes which was more pronounced in the constructed-wetland system.

Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments.

Macroalgae, commonly known as seaweed, are foundational species in coastal ecosystems and contribute significantly to coastal primary production globally. However, the impact of macroalgal decomposition on benthic biological nitrogen fixation (BNF) after deposition to the seafloor remains largely unexplored. In this study, we measure BNF rates at three different sites at the Big Fisherman's Cove on Santa Catalina Island, CA, USA, which is representative of globally distributed rocky bottom macroalgal habitats. Unamended BNF rates varied among sites (0.001-0.05 nmol N g-1 h -1) and were generally within the lower end of previously reported ranges. We hypothesized that the differences in BNF between sites were linked to the availability of organic matter. Indeed, additions of glucose, a labile carbon source, resulted in 2-3 orders of magnitude stimulation of BNF rates in bottle incubations of sediment from all sites. To assess the impact of complex, autochthonous organic matter, we simulated macroalgal deposition and remineralization with additions of brown (i.e., Macrocystis pyrifera and Dictyopteris), green (i.e., Codium fragile), and red (i.e., Asparagopsis taxiformis) macroalgae. While brown and green macroalgal amendments resulted in 53- to 520-fold stimulation of BNF rates-comparable to the labile carbon addition-red alga was found to significantly inhibit BNF rates. Finally, we employed nifH sequencing to characterize the diazotrophic community associated with macroalgal decomposition. We observed a distinct community shift in potential diazotrophs from primarily Gammaproteobacteria in the early stages of remineralization to a community dominated by Deltaproteobacteria (e.g., sulfate reducers), Bacteroidia, and Spirochaeta toward the latter phase of decomposition of brown, green, and red macroalgae. Notably, the nifH-containing community associated with red macroalgal detritus was distinct from that of brown and green macroalgae. Our study suggests coastal benthic diazotrophs are limited by organic carbon and demonstrates a significant and phylum-specific effect of macroalgal loading on benthic microbial communities.

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments.

Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.

Seasonal dynamics response mechanism of benthic microbial community to artificial reef habitats

Artificial reefs (ARs) have been globally deployed to enhance and restore coastal resource and ecosystems. Microorganisms play an essential role in marine ecosystems, while the knowledge regarding the impact of ARs on microecology is still limited, particularly data concerning the response of benthic microbial community to AR habitats. In this study, the seasonal dynamics of benthic microbial community in AR and adjacent non-artificial reef (NAR) areas surrounding Xiaoshi Island were investigated with high-throughput sequencing technology. The results revealed that the diversity and structure of microbial community between AR and NAR both displayed pronounced seasonal dynamics. There was a greater influence of season factors on microbial communities than that of habitat type. The microbial communities in AR and NAR habitats were characterized by a limited number of abundant taxa (ranging from 5 to 12 ASVs) with high relative abundance (8.35–25.53%) and numerous rare taxa (from 5994 to 12412 ASVs) with low relative abundance (11.91%–24.91%). Proteobacteria, Bacteroidota and Desulfobacterota were the common predominant phyla, with the relative abundances ranging from 50.94% to 76.76%. A total of 52 biomarkers were discovered, with 15, 4, 6, and 27 biomarkers identified in spring, summer, autumn and winter, respectively. Co-occurrence network analysis indicated that AR displayed a more complex interaction pattern and higher susceptibility to external disturbances. Furthermore, the neutral model and βNTI analyses revealed that the assembly of microbial communities in both AR and NAR is significantly influenced by stochastic processes. This study could provide valuable insights into the impact of ARs construction on the benthic ecosystems and would greatly facilitate the development and implementation of the future AR projects.

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort

Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Polar lake microbiomes have distinct evolutionary histories.

Toward the poles, life on land is increasingly dominated by microorganisms, yet the evolutionary origin of polar microbiomes remains poorly understood. Here, we use metabarcoding of Arctic, sub-Antarctic, and Antarctic lacustrine benthic microbial communities to test the hypothesis that high-latitude microbiomes are recruited from a globally dispersing species pool through environmental selection. We demonstrate that taxonomic overlap between the regions is limited within most phyla, even at higher-order taxonomic levels, with unique deep-branching phylogenetic clades being present in each region. We show that local and regional taxon richness and net diversification rate of regionally restricted taxa differ substantially between polar regions in both microeukaryotic and bacterial biota. This suggests that long-term evolutionary divergence resulting from low interhemispheric dispersal and diversification in isolation has been a prominent process shaping present-day polar lake microbiomes. Our findings illuminate the distinctive biogeography of polar lake ecosystems and underscore that conservation efforts should include their unique microbiota.

Drivers of pelagic and benthic microbial communities on Central Arctic seamounts

Seamounts are abundant features on the seafloor that serve as hotspots and barriers for the dispersal of benthic organisms. The primary focus of seamount ecology has typically been on the composition and distribution of faunal communities, with far less attention given to microbial communities. Here, we investigated the microbial communities in the water column (0-3400 m depth) and sediments (619-3883 m depth, 0-16 cm below seafloor) along the ice-covered Arctic ridge system called the Langseth Ridge. We contextualized the microbial community composition with data on the benthic trophic state (i.e., organic matter, chlorophyll-a content, and porewater geochemistry) and substrate type (i.e., sponge mats, sediments, basaltic pebbles). Our results showed slow current velocities throughout the water column, a shift in the pelagic microbial community from a dominance of Bacteroidia in the 0-10 m depth towards Proteobacteria and Nitrososphaeria below the epipelagic zone. In general, the pelagic microbial communities showed a high degree of similarity between the Langseth Ridge seamounts to a northern reference site. The only notable differences were decreases in richness between ~600 m and the bottom waters (~10 m above the seafloor) that suggest a pelagic-benthic coupling mediated by filter feeding of sponges living on the seamount summits. On the seafloor, the sponge spicule mats, and polychaete worms were the principal source of variation in sedimentary biogeochemistry and the benthic microbial community structure. The porewater signature suggested that low organic matter degradation rates are accompanied by a microbial community typical of deep-sea oligotrophic environments, such as Proteobacteria, Acidimicrobiia, Dehalococcoidia, Nitrospira, and archaeal Nitrososphaeria. The combined analysis of biogeochemical parameters and the microbial community suggests that the sponges play a significant role for pelagic-benthic coupling and acted as ecosystem engineers on the seafloor of ice-covered seamounts in the oligotrophic central Arctic Ocean.

Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China

Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0–20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0–295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0–135 cm) and deep sediments (155–295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.

Linkages between organic carbon composition and microbial community structure in two contrasting subtropical mangrove sediments in southern China

Terrestrial and marine derived organic carbon (OC) accumulated in coastal mangrove sediment affect the structure of the benthic microbial community. This study collected sediment cores from subtropical coastal Xiwan and Maipo mangrove in southern China to study the linkages between the sedimentary OC and microbial community structure. The Maipo sediments showed more TOC (2.20 ± 0.20 vs. 1.67 ± 0.35 %), slightly depleted δ13C(−25.59 ± 0.71 vs. −25.07 ± 1.46 ‰), higher average Chl-a (62.25 ± 30.74 vs. 34.65±12.92μg/g TOC) and lignin (3.14 ± 2.21 vs. 1.80 ± 0.80 mg/100 mg TOC) content mostly due to larger coverage area of mangrove forests than coastal Xiwan sediment. While the dominate bacteria phylum and archaea class were the same, the microbes stratified to top, middle​ and bottom community with depths. The two cores also showed different indicator species and relative microbial abundance. Certain bacteria and archaea were positively correlated with the phenolic compounds indicating their involvement in lignin degradation. Therefore, different OC sources and decomposition status could be crucial shaping the microbial community.

Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts.

Glacier recession is creating new water bodies in proglacial forelands worldwide, including Antarctica. Yet, it is unknown how microbial communities of recently formed "young" waterbodies (originating decades to a few centuries ago) compare with established "old" counterparts (millennia ago). Here, we compared benthic microbial communities of different lake types on James Ross Island, Antarctic Peninsula, using 16S rDNA metabarcoding and light microscopy to explore bacterial and diatom communities, respectively. We found that the older lakes host significantly more diverse bacterial and diatom communities compared to the young ones. To identify potential mechanisms for these differences, linear models and dbRDA analyses suggested combinations of water temperature, pH, and conductivity to be the most important factors for diversity and community structuring, while differences in geomorphological and hydrological stability, though more difficult to quantify, are likely also influential. These results, along with an indicator species analysis, suggest that physical and chemical constraints associated with individual lakes histories are likely more influential to the assembly of the benthic microbial communities than lake age alone. Collectively, these results improve our understanding of microbial community drivers in Antarctic freshwaters, and help predict how the microbial landscape may shift with future habitat creation within a changing environment.

The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments.

The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.

Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities

Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.

Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.

A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.