Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA

Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ13C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42- and NO3- as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.

Responses of methane production and methanogenic pathways to polystyrene nanoplastics exposure in paddy soil

Nanoplastics (NPs) have attracted increasing attention within terrestrial ecosystems. However, our understanding of their impacts on the intricate anaerobic methanogenesis processes occurring in paddy soils microbial communities remains limited with respect to nanoplastics shape, function, and metabolic effects. Herein, we explored the effects of polystyrene nanoplastics (PS-NPs) and microplastics (PS-MPs) on anaerobic methanogenesis in a typical paddy soil. The results show that PS-NPs delayed methane production and the time to reach peak acetate content in incubation process of paddy soils, and the methanogenic rate increased rapidly after 13 days, with a maximum increase of 87.97%. However, PS-MPs had no marked effect on CH4, CO2 and acetate production. In addition, PS-NPs affected soil physicochemical properties by reducing pH and increasing electrical conductivity. Acetoclastic methanogens were enriched and the relative abundance of the genes ackA, pta, ACSS, cdhC, cdhD and cdhE in the acetoclastic pathways were significantly increased under PS-NPs exposure. In addition, PS-MPs had significant effect on the microbial community structure but no effect on methanogenic pathways of the paddy soils. This study provides important insights into the response of key microorganisms, functional genes and methanogenesis pathways to NPs during anaerobic methanogenesis in paddy soils.

A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00212-y.

Four years of climate warming reduced dark carbon fixation in coastal wetlands

Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a 4-yr field warming experiment (average annual temperature increase of 1.5°C), DCF rates were observed to be significantly inhibited by warming in coastal wetlands (average annual DCF decline of 21.6%, and estimated annual loss of 0.08-1.5 Tg C yr-1 in global coastal marshes), thus causing a positive climate feedback. Under climate warming, chemoautotrophic microbial abundance and biodiversity, which were jointly affected by environmental changes such as soil organic carbon and water content, were recognized as significant drivers directly affecting DCF rates. Metagenomic analysis further revealed that climate warming may alter the pattern of DCF carbon sequestration pathways in coastal wetlands, increasing the relative importance of the 3-hydroxypropionate/4-hydroxybutyrate cycle, whereas the relative importance of the dominant chemoautotrophic carbon fixation pathways (Calvin-Benson-Bassham cycle and W-L pathway) may decrease due to warming stress. Collectively, our work uncovers the feedback mechanism of microbially mediated DCF to climate warming in coastal wetlands, and emphasizes a decrease in carbon sequestration through DCF activities in this globally important ecosystem under a warming climate.

Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China

Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 10⁵ to 10⁷ copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.

Dark carbon fixation in intertidal sediments: Controlling factors and driving microorganisms

Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y^-1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using ¹⁴C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m^-2 day^-1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM-harboring bacteria, rather than cbbL-harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM-harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus, and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands.

DHA-Rich Aurantiochytrium Biomass, a Novel Dietary Supplement, Resists Degradation by Rumen Microbiota without Disrupting Microbial Activity

We first sought to evaluate the effect of dietary supplementation with the docosahexaenoic acid (DHA)-rich microalgae, Aurantiochytrium limacinum (AURA), on rumen fermentation and the resistance of DHA to degradation and biohydrogenation by rumen microbes through ex vivo fermentation experiments. Subsequently, we sought to quantify the diet-derived DHA content of milk and the impact of AURA on microbial composition and metabolism in a pilot feeding trial with rumen-cannulated dairy cows. To achieve our aims, rumen fluid from cannulated cows was used as inoculum, and the effect of AURA inclusion on fermentation ex vivo was examined. At doses corresponding to the amount of AURA recommended for commercial production animals, only ~10% of DHA was degraded or biohydrogenated by rumen microorganisms. The results show that feeding with AURA had no effect on either total bacterial density or short-chain fatty acid production. Real-time quantitative PCR analysis of the rumen fluid samples collected during a seven-week in vivo trial revealed that microbes related to lactic acid metabolism and methanogenesis were significantly suppressed by the AURA-supplemented diet. The DHA concentration in milk increased over 25-fold with the AURA-supplemented diet and dropped by 30–40% within one week of washout. The addition of A. limacinum biomass to dairy cow diets resulted in positive effects on rumen microbial composition with no adverse effect on fermentation activity. AURA-derived DHA was stable, with only modest degradation in the rumen, and was successfully deposited in milk. This is the first study to investigate the effect of supplementing the diet of dairy cows with a protist-based biomass, namely, on important rumen fermentation parameters and on DHA deposition in milk, using a combination of ex vivo and in vivo approaches.

Variations in bacterial and archaeal community structure and diversity along the soil profiles of a peatland in Southwest China

As bacteria and archaea are key components in the ecosystem, information on their dynamics in soil profiles is important for understanding the biogeochemical cycles in peatlands. However, little is known about the vertical distribution patterns of bacteria and archaea in the Bitahai peatland, or about their relationships with soil chemical properties. Here, bacterial and archaeal abundance, diversity, and composition of the Bitahai peatlands at 0-100 cm soil depths were analyzed by sequencing of 16S rRNA genes (Illumina, MiSeq). Soil pH, total C, N, and P concentrations and stoichiometric ratios were also estimated. The results revealed that total C and total N contents, as well as C:P and N:P ratios, significantly increased with increasing peatland soil depths, while total P decreased. The top three dominant phyla were Proteobacteria (39.64%), Acidobacteria (12.93%), and Chloroflexi (12.81%) in bacterial communities, and were Crenarchaeota (58.67%), Thaumarchaeota (14.34%), and Euryarchaeota (10.82%) in archaeal communities in the Bitahai peatland, respectively. The total relative abundance of methanogenic groups and ammonia-oxidizing microorganisms all significantly decreased with soil depth. Both bacterial and archaeal diversities were significantly affected by the soil depth. Soil C, N, and P concentrations and stoichiometric ratios markedly impacted the community structure and diversity in archaea, but not in bacteria. Therefore, these results highlighted that the microbial community structure and diversity depended on soil depth for the Bitahai peatlands, and the factors affecting bacteria and archaea in the Bitahai peatlands were different.

Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.

Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment

Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below.

Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH₄) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NO_x) on methanogenic activity are known from pure culture studies, the role of NO_x in the methane cycling of peatlands remains unexplored. Here, we investigated the CH₄ content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NO_x and nitrous oxide (N₂O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and ¹³C enrichment in dissolved inorganic carbon and CH₄ pools, which are primarily contingent on H₂-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NO_x cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NO_x. Experiments testing the interaction of NO_x species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N₂O (complete inhibition), which would act as an unaccounted CH₄ control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH₄ fluxes.

Vertical diversity and association pattern of total, abundant and rare microbial communities in deep-sea sediments

Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.

Methane emissions respond to soil temperature in convergent patterns but divergent sensitivities across wetlands along altitude

Among the global coordinated patterns in soil temperature and methane emission from wetlands, a declining trend of optimal soil temperature for methane emissions from low to high latitudes has been witnessed, while the corresponding trend along the altitudinal gradient has not yet been investigated. We therefore selected two natural wetlands located at contrasting climatic zones from foothill and mountainside of Nepal Himalayas, to test: (1) whether the optimal temperature for methane emissions decreases from low to high altitude, and (2) whether there is a difference in temperature sensitivity of methane emissions from those wetlands. We found significant spatial and temporal variation of methane emissions between the two wetlands and seasons. Soil temperature was the dominant driver for seasonal variation in methane emissions from both wetlands, though its effect was perplexed by the level of standing water, aquatic plants, and dissolved organic carbon, particularly in the deep water area. When integrative comparison was conducted by adding the existing data from wetlands of diverse altitudes, and the latitude-for-altitude effect was taken into account, we found the baseline soil temperatures decrease whilst the altitude rises with respect to a rapid increase in methane emission from all wetlands, however, remarkably higher sensitivity of methane emissions to soil temperature (apparent Q₁₀ ) was found in mid-altitude wetland. We provide the first evidence of an apparent decline in optimal temperature for methane emissions with increasing elevation. These findings suggest a convergent pattern of methane emissions with respect to seasonal temperature shifts from wetlands along altitudinal gradient, while a divergent pattern in temperature sensitivities exhibits a single peak in mid-altitude.

Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition

Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.

On-farm soil resistome is modified after treating dairy calves with the antibiotic florfenicol

We determined the immediate impact of exposure to antibiotic-treated animals on housing soil microbiome and resistome. Fecal (n = 36) and soil (n = 108) samples from dairy calves (n = 6) treated with and without florfenicol over 30 days were collected. There were temporary changes in the gut microbiome of antibiotic-treated calves as measured by Shannon diversity (16S rRNA gene sequencing; P = 0.03), but not in the housing soil microbiome (P > 0.05). Droplet-digital PCR demonstrated that floR gene increased by 1-log in soil exposed to treated animals (P < 0.001), but it remained relatively stable in the control soil whereby calves were not treated with antibiotic. Resistome in exposed soil was largely modified (P = 0.004) with the overall prevalence of antimicrobial resistance genes (ARGs) significantly elevated (3.8-fold increase by day 10; P = 0.01). In addition to florfenicol, enriched ARGs collectively conferring resistance to tetracyclines, aminoglycosides, sulfonamides, elfamycins, macrolides-lincosamides-streptrogramin A/B, and beta-lactams. Quantitative PCR validated that ARGs including str and tetG in soil exposed to florfenicol-treated calves had gradually increased fold-change difference relative to the control soil over time. Moreover, a greater diversity of transferrable ARGs was observed in exposed soil and these were associated with a greater diversity of bacterial species. Evaluation of on-farm effects to soil in situ after exposure to antibiotic-treated animals can help design effective managements to mitigate antibiotic resistance in food-animal production.

Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions

Despite the risks that hydrocarbon contamination from pipeline leaks or train derailments impose on the health of peatlands in hydrocarbon production areas and transportation corridors, assessing the effect of such contaminations on the health and sustainability of peatlands has received little attention. This study investigates the impacts of hydrocarbons on peat microbial communities. Column experiments were conducted on non-aqueous phase liquid (NAPL) contaminated undisturbed peat core (0-35 cm) under static and fluctuating water table conditions. Water table fluctuations reduced residual NAPL saturation from 8.1-11.3% to 7.7-9.5%. Biodegradation of n-C₈ and n-C₁₂ along with oxidation of CH₄ together produced high CO₂ concentrations in the headspace. Clear patterns in dynamics in the microbial community structure were observed, with a more pronounced population growth. However, a significant loss of microbial richness was observed in contaminated columns. The result indicates that the phylum Proteobacteria benefited most from NAPL; however, their families differed between static and fluctuating water table conditions. This study established strong evidence that peat microbes and water table fluctuation can be an excellent tool for hydrocarbon removal and its control in peatlands.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.

Changes in Methane Emission and Community Composition of Methane-Cycling Microorganisms Along an Elevation Gradient in the Dongting Lake Floodplain, China

Methane (CH4) emission and environmental controls of CH4-cycling microorganisms are unclear in inland floodplains. Here, we examined soil CH4 emissions and the community composition of CH4-cycling microorganisms under three vegetation types—mudflat (MF, no vegetation cover), Carex meadow (CM, mainly Carex brevicuspis), and reed land (RL, mainly Miscanthus sacchariflorus)—from water-adjacent areas to higher-elevation land in the Dongting Lake floodplain, China. The results showed that CH4 emission is the highest in CM, while significant absorption was observed in the RL site. The abundance ratio of methanogen/methanotroph was the highest in CM, intermediate in MF, and lowest in RL. The Methanosarcinaceae family represented the dominant methanogens in the three sampling sites (41.32–75.25%). The genus Methylocystis (60.85%, type II methanotrophs) was dominant in CM, while Methylobacter and Methylosarcina (type I methanotrophs) were the dominant genera in MF (51.00%) and RL (50.24%), respectively. Structural equation model analysis showed that methanogen and methanotroph abundance were affected by water table depth, soil water content, and pH indirectly through soil organic content, total nitrogen, microbial biomass carbon, and microbial biomass nitrogen. These results indicated that the Dongting Lake floodplain may change from a CH4 source to a CH4 sink with vegetation succession with an increase in elevation, and the methanogen/methanotroph ratio can be used as a proxy for CH4 emission in wetland soils. The continuous increase in reed area combined with the decrease in Carex meadow may mitigate CH4 emission and enhance the CH4 sink function during the non-flood season in the Dongting Lake floodplain.

Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir

Nitrite (NO₂^-)- and nitrate (NO₃^-)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO₂^-- and NO₃^--dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 10⁷ to 2.8 × 10⁸ copies g^-1 dry sediment) than upstream sediments (2.4 × 10⁷ to 3.5 × 10⁷ copies g^-1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 10⁵ to 4.8 × 10⁵ copies g^-1 dry sediment). The ¹³CH₄ tracer experiments suggested the occurrence of NO₂^-- and NO₃^--dependent AOM activities, and their rates were 4.7-14.1 and 0.8-2.6 nmol CO₂ g^-1 (dry sediment) d^-1, respectively. Further, the rates of NO₂^--dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO₃^- concentration was the key factor affecting the spatial variations of abundance and activity of NO₂^--dependent anaerobic methanotrophs. Overall, our results showed different responses of NO₂^-- and NO₃^--dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.

Macrofaunal control of microbial community structure in continental margin sediments

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O₂ introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.

Eutrophication as a driver of microbial community structure in lake sediments

Lake sediments are globally important carbon sinks. Although the fate of organic carbon in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matter (OM) sources in sediments, on microbial communities across five lakes in central Switzerland. Lipid biomarkers and distributions of microbial respiration reactions indicate strong increases in aquatic OM contributions and microbial activity with increasing trophic state. Across all lakes, 16S rRNA genes analyses indicate similar depth-dependent zonations at the phylum- and class-level that follow vertical distributions of OM sources and respiration reactions. Yet, there are notable differences, such as higher abundances of nitrifying Bacteria and Archaea in an oligotrophic lake. Furthermore, analyses at the order-level and below suggest that changes in OM sources due to eutrophication cause permanent changes in bacterial community structure. By contrast, archaeal communities are differentiated according to trophic state in recently deposited layers, but converge in older sediments deposited under different trophic regimes. Our study indicates an important role for trophic state in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of sediment Bacteria and Archaea to eutrophication.

Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship

Studies of marine benthic archaeal communities are updating our view of their taxonomic composition and metabolic versatility. However, large knowledge gaps remain with regard to community assembly processes and inter taxa associations. Here, using 16S rRNA gene amplicon sequencing and qPCR, we investigated the spatiotemporal dynamics, assembly processes, and co-occurrence relationships of the archaeal community in 58 surface sediment samples collected in both summer and winter from across ~1500 km of the eastern Chinese marginal seas. Clear patterns in spatiotemporal dynamics in the archaeal community structure were observed, with a more pronounced spatial rather than seasonal variation. Accompanying the geographic variation was a significant distance-decay pattern with varying contributions from different archaeal clades, determined by their relative abundance. In both seasons, dispersal limitation was the most important process, explaining ~40% of the community variation, followed by homogeneous selection and ecological drift, that made an approximately equal contribution (~30%). This meant that stochasticity rather than determinism had a greater impact on the archaeal community assembly. Furthermore, we observed seasonality in archaeal co-occurrence patterns: closer inter-taxa connections in winter than in summer, and unmatched geographic patterns between community composition and co-occurrence relationship. These results demonstrate that the benthic archaeal community was assembled under a seasonal-consistent mechanism but the co-occurrence relationships changed over the seasons, indicating complex archaeal dynamic patterns in coastal sediments of the eastern Chinese marginal seas.

Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia

Tropical peatlands are globally important carbon reservoirs that play a crucial role in fluxes of atmospheric greenhouse gases. Amazon peatlands are expected to be large source of atmospheric methane (CH₄) emissions, however little is understood about the rates of CH₄ flux or the microorganisms that mediate it in these environments. Here we studied a mineral nutrient gradient across peatlands in the Pastaza-Marañón Basin, the largest tropical peatland in South America, to describe CH₄ fluxes and environmental factors that regulate species assemblages of methanogenic and methanotrophic microorganisms. Peatlands were grouped as minerotrophic, mixed and ombrotrophic categories by their general water source leading to different mineral nutrient content (rich, mixed and poor) quantified by trace elements abundance. Microbial communities clustered dependent on nutrient content (ANOSIM p < 0.001). Higher CH₄ flux was associated with minerotrophic communities compared to the other categories. The most dominant methanogens and methanotrophs were represented by Methanobacteriaceae, and Methylocystaceae, respectively. Weighted network analysis demonstrated tight clustering of most methanogen families with minerotrophic-associated microbial families. Populations of Methylocystaceae were present across all peatlands. Null model testing for species assemblage patterns and species rank distributions confirmed non-random aggregations of Methylococcacae methanotroph and methanogen families (p < 0.05). We conclude that in studied amazon peatlands increasing mineral nutrient content provides favorable habitats for Methanobacteriaceae, while Methylocystaceae populations seem to broadly distribute independent of nutrient content.

Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context

The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.

Dairy farm soil presents distinct microbiota and varied prevalence of antibiotic resistance across housing areas

Dairy cattle of different ages experience different living conditions and varied frequency of antibiotic administration that likely influence the distribution of microbiome and resistome in ways that reflect different risks of microbial transmission. To assess the degree of variance in these distributions, fecal and soil samples were collected from six distinct housing areas on commercial dairy farms (n = 7) in Washington State. 16S rRNA gene sequencing indicated that the microbiota differed between different on-farm locations in feces and soil, and in both cases, the microbiota of dairy calves was often distinct from others (P < 0.05). Thirty-two specific antibiotic resistance genes (ARGs) were widely distributed on dairies, of which several clinically relevant ARGs (including cfr, cfrB, and optrA) were identified for the first time at U.S. dairies. Overall, ARGs were observed more frequently in feces and soil from dairy calves and heifers than from hospital, fresh, lactation and dry pens. Droplet-digital PCR demonstrated that the absolute abundance of floR varied greatly across housing areas and this gene was enriched the most in calves and heifers. Furthermore, in an extended analysis with 14 dairies, environmental soils in calf pens had the most antibiotic-resistant Escherichia coli followed by heifer and hospital pens. All soil E. coli isolates (n = 1,905) are resistant to at least 4 different antibiotics, and the PFGE analysis indicated that florfenicol-resistant E. coli is probably shared across geographically-separated farms. This study identified a discrete but predictable distribution of antibiotic resistance genes and organisms, which is important for designing mitigation for higher risk areas on dairy farms.

Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.

Improving the Accuracy of Flow Cytometric Quantification of Microbial Populations in Sediments: Importance of Cell Staining Procedures

The accuracy of flow cytometric (FCM) quantifications of microbial populations in sediments varies with FCM settings, cell extraction and staining protocols, as well as sample types. In the present study, we improve the accuracy of FCM for enumerating microorganisms inhabiting diverse lake and marine sediment types based on extensive tests with FCM settings, extraction buffer chemical compositions, cell separation methods, and staining procedures. Tests on the FCM settings, (e.g., acquisition time, rates of events) and salinity of extraction solutions show minor impacts on FCM enumerations and yields of cell extraction, respectively. Existing methods involving hydrofluoric acid (HF) treatment to release sediment-attached cells into solution prove effective on both marine and freshwater samples. Yet, different staining techniques (direct staining of cell extracts, staining of membrane-filtered cell extracts) produce clear differences in cell number estimates. We demonstrate that, while labor-intensive membrane-staining generates high cell staining efficiency and accurate cell counts that are consistent across FCM and epifluorescence microscopy-based (EFM) quantification methods, accurate cell counts determined by more time- and labor-efficient direct staining require consideration of dye concentration, sample dilution, and lithology. Yet, good agreement between the two staining methods can be achieved through sample-specific adjustments of dye concentrations and sample dilutions during direct staining. We thus present a complete protocol for FCM-based cell quantification, that includes all steps from the initial sample fixation to the final enumeration, with recommendations for buffer compositions, direct and membrane-based staining procedures, and the final FCM assay. This protocol is versatile, accurate, and reliable, as is evident from good agreement with cell quantifications by EFM and quantitative polymerase chain reaction (qPCR) of 16S rRNA genes across a wide range of sedimentary sample types.

The impact of urbanisation on community structure, gene abundance and transcription rates of microbes in upland swamps of Eastern Australia

The Temperate Highland Peat Swamps on Sandstone of the Sydney Basin occur in the headwaters of Sydney's drinking water catchments and are listed as endangered ecosystems, yet they have suffered habitat losses and degradation due to human impacts such as urbanisation. Despite ongoing efforts to restore and better protect upland swamps, they remain poorly understood, potentially hindering the effectiveness of management efforts. Essential to overall ecosystem function and the provision of services for human and environmental benefit are the microbial component of wetland ecosystems. In the case of these swamps, the microbes, have not yet been studied. Here, we investigated differences in the microbial community of upland swamps in urbanised catchments compared to swamps from natural catchments in the Blue Mountains. A total of twelve swamps were sampled, six from within urbanised catchments and six with intact vegetation catchments, to compare sediment conditions and microbial community and genes expression and abundances. Catchment impervious area and number of stormwater drains entering a swamp, indicators for urbanisation, positively correlated with the pH and ammonium concentration of swamp sediment. Community analysis of the 16S rRNA gene (T-RFLP, qPCR) revealed the elevated pH of urbanised swamps coincided with changes to the abundance of bacteria and archaea. Furthermore, RT-qPCR revealed genes involved in carbon cycling (mcrA & pmoA) were more likely to be found in urbanised swamps. Taken together, our results indicate that urbanisation of the Blue Mountains is impacting the environmental services provided by the microbial community of upland swamps in the Sydney Basin.

Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth

Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.

Active pathways of anaerobic methane oxidation across contrasting riverbeds

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO₂ g⁻¹ (dry sediment) d⁻¹, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 10⁵ to 1.5 × 10⁷ and 2.1 × 10⁴ to 2.5 × 10⁵ copies g⁻¹ dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.

Cryptic CH4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea

Methane in the seabed is mostly oxidized to CO₂ with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO₂ by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 10⁸ to 10⁶ cells cm^-3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 10⁸ cells cm^-3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %T_AAC (percentage of total organic carbon present as amino acid carbon), %T_AAN (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site

The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.

Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy)

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.

Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China

Wetlands are an important methane (CH₄) emission source. CH₄ is mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are overwhelmingly dominant in high moisture samples, while Methylocystis (53.3%) and Methylomonas (42.2%) belonging to types II and I methanotrophs are the predominant groups in low moisture samples. Furthermore, qPCR analysis revealed that the abundance of methanogens and methanotrophs were higher in high moisture samples than that in low moisture samples. Overall, this comparative study between wetlands controlled by two different water regimes on the Qinghai-Tibetan Plateau provides fundamental data for further research on microbial functions within extreme ecosystems.

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.

Microbial turnover times in the deep seabed studied by amino acid racemization modelling

The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D:L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D:L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments. We applied for the first time newly established constraints on several important input parameters of the D:L-amino acid model, such as a higher aspartic acid racemization rate constant and a lower cell-specific carbon content of sub-seafloor microorganisms. Our model results show that the pool of necromass amino acids is turned over by microbial activity every few thousand years, while the turnover times of vegetative cells are in the order of years to decades. Notably, microbial turnover times in million-year-old sediment from the Peru Margin are up to 100-fold shorter than previous estimates, highlighting the influence of microbial activities on element cycling over geologic time scales.

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2

The effects of elevated atmospheric CO₂ concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO₂ in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO₂ (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO₂ increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO₂. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO₂. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO₂.

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy

Biochemical pathways of methanogenesis and methanotrophy coupled with carbon (C)-nitrogen (N) metabolism were studied in long term (13years) manured systems in lowland rice paddy through metagenomics approach. Manured systems included in this study were, control (exclusion of application of any manure), farm yard manure (FYM, @5Mgha^-1yr^-1) and green manuring (GM with Sesbania aculeata). Metagenomic sequence data revealed the dominance of C decomposing bacterial communities' like Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Acidobacteria, in manure amended soils as compared to control. Diversities for assimilatory and dissimilatory N-fixing microorganisms at phylum level were found higher under GM as compared to rest. Two genera responsible for methanogenesis, viz. Methanolobus and Methanotorris were absent in manured systems as compared to control. The acetoclastic and serine pathway was found as the predominant pathway for methanogenesis and methanotrophy, respectively, in tropical lowland rice paddy. Abundance reads of enzymes were in the range of 254-445 in the acetoclastic methanogenesis pathway. On the other hand, these were varied from 165 to 216 in serine pathway of methanotrophy. Lowland paddy soil exhibited higher functional and structural diversities in manured systems as compared to unamended control in respect to labile C pools and CH₄ production. Methane (CH₄) emission was 31% higher in FYM system than GM. However, nitrous oxide (N₂O) emission was found 25% higher in GM as compared to FYM. As a whole, bacterial diversities were higher under FYM system in tropical lowland rice paddy as compared to GM and unamended systems.

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

Nitrate- and nitrite-dependent anaerobic oxidation of methane

Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N₂ and O₂ for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.

Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem

Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., NO3−, NH4+), salinity and pH (explaining 73.8% of the total variation, R² = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, NO3−, NH4+ and SO42−, across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.