Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils

Temporal patterns of bacterial communities in the Billings Reservoir system

In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4-2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.

Coordination and divergence in community assembly processes across co-occurring microbial groups separated by cell size

Setting the pace of life and constraining the role of members in food webs, body size can affect the structure and dynamics of communities across multiple scales of biological organization (e.g., from the individual to the ecosystem). However, its effects on shaping microbial communities, as well as underlying assembly processes, remain poorly known. Here, we analyzed microbial diversity in the largest urban lake in China and disentangled the ecological processes governing microbial eukaryotes and prokaryotes using 16S and 18S amplicon sequencing. We found that pico/nano-eukaryotes (0.22-20 μm) and micro-eukaryotes (20-200 μm) showed significant differences in terms of both community composition and assembly processes even though they were characterized by similar phylotype diversity. We also found scale dependencies whereby micro-eukaryotes were strongly governed by environmental selection at the local scale and dispersal limitation at the regional scale. Interestingly, it was the micro-eukaryotes, rather than the pico/nano-eukaryotes, that shared similar distribution and community assembly patterns with the prokaryotes. This indicated that assembly processes of eukaryotes may be coupled or decoupled from prokaryotes' assembly processes based on eukaryote cell size. While the results support the important influence of cell size, there may be other factors leading to different levels of assembly process coupling across size classes. Additional studies are needed to quantitatively parse the influence of cell size versus other factors as drivers of coordinated and divergent community assembly processes across microbial groups. Regardless of the governing mechanisms, our results show that there are clear patterns in how assembly processes are coupled across sub-communities defined by cell size. These size-structured patterns could be used to help predict shifts in microbial food webs in response to future disturbance.

Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land

Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides. We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.

Microbial iron cycling is prevalent in water-logged Alaskan Arctic tundra habitats, but sensitive to disturbance

Water logged habitats in continuous permafrost regions provide extensive oxic-anoxic interface habitats for iron cycling. The iron cycle interacts with the methane and phosphorus cycles, and is an important part of tundra biogeochemistry. Our objective was to characterize microbial communities associated with the iron cycle within natural and disturbed habitats of the Alaskan Arctic tundra. We sampled aquatic habitats within natural, undisturbed and anthropogenically disturbed areas and sequenced the 16S rRNA gene to describe the microbial communities, then supported these results with process rate and geochemical measurements. Undisturbed habitats have microbial communities that are significantly different than disturbed habitats. Microbial taxa known to participate in the iron and methane cycles are significantly associated with natural habitats, whereas they are not significantly associated with disturbed sites. Undisturbed habitats have significantly higher extractable iron and are more acidic than disturbed habitats sampled. Iron reduction is not measurable in disturbed aquatic habitats and is not stimulated by the addition of biogenic iron mats. Our study highlights the prevalence of Fe-cycling in undisturbed water-logged habitats, and demonstrates that anthropogenic disturbance of the tundra, due to legacy gravel mining, alters the microbiology of aquatic habitats and disrupts important biogeochemical cycles in the Arctic tundra.

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.

Functional microbial ecology in arctic soils: the need for a year-round perspective

The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.

Methanogenic Community, CH4 Production Potential and Its Determinants in the Active Layer and Permafrost Deposits on the Tibetan Plateau

Permafrost thaw could increase methane (CH4) emissions, which largely depends on CH4 production driven by methanogenic archaea. However, large-scale evidence regarding key methanogenic taxa and their relative importance to abiotic factors in mediating methanogenesis remains limited. Here, we explored the methanogenic community, potential CH4 production and its determinants in the active layer and permafrost deposits based on soil samples acquired from 12 swamp meadow sites along a ∼1000 km permafrost transect on the Tibetan Plateau. Our results revealed lower CH4 production potential, mcrA gene abundance, and richness in the permafrost layer than those in the active layer. CH4 production potential in both soil layers was regulated by microbial and abiotic factors. Of the microbial properties, marker OTUs, rather than the abundance and diversity of methanogens, stimulated CH4 production potential. Marker OTUs differed between the two soil layers with hydrogenotrophic Methanocellales and facultative acetoclastic Methanosarcina predominant in regulating CH4 production potential in the permafrost and active layer, respectively. Besides microbial drivers, CH4 production potential increased with the carbon/nitrogen (C/N) ratio in both soil layers and was also stimulated by soil moisture in the permafrost layer. These results provide empirical evidence for model improvements to better predict permafrost carbon feedback to climate warming.

Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic

Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens - mcrA gene and diazotrophs - nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

Temporal, Spatial, and Temperature Controls on Organic Carbon Mineralization and Methanogenesis in Arctic High-Centered Polygon Soils

Warming temperatures in continuous permafrost zones of the Arctic will alter both hydrological and geochemical soil conditions, which are strongly linked with heterotrophic microbial carbon (C) cycling. Heterogeneous permafrost landscapes are often dominated by polygonal features formed by expanding ice wedges: water accumulates in low centered polygons (LCPs), and water drains outward to surrounding troughs in high centered polygons (HCPs). These geospatial differences in hydrology cause gradients in biogeochemistry, soil C storage potential, and thermal properties. Presently, data quantifying carbon dioxide (CO₂) and methane (CH₄) release from HCP soils are needed to support modeling and evaluation of warming-induced CO₂ and CH₄ fluxes from tundra soils. This study quantifies the distribution of microbial CO₂ and CH₄ release in HCPs over a range of temperatures and draws comparisons to previous LCP studies. Arctic tundra soils were initially characterized for geochemical and hydraulic properties. Laboratory incubations at −2, +4, and +8°C were used to quantify temporal trends in CO₂ and CH₄ production from homogenized active layer organic and mineral soils in HCP centers and troughs, and methanogen abundance was estimated from mcrA gene measurements. Results showed that soil water availability, organic C, and redox conditions influence temporal dynamics and magnitude of gas production from HCP active layer soils during warming. At early incubation times (2–9 days), higher CO₂ emissions were observed from HCP trough soils than from HCP center soils, but increased CO₂ production occurred in center soils at later times (>20 days). HCP center soils did not support methanogenesis, but CH₄-producing trough soils did indicate methanogen presence. Consistent with previous LCP studies, HCP organic soils showed increased CO₂ and CH₄ production with elevated water content, but HCP trough mineral soils produced more CH₄ than LCP mineral soils. HCP mineral soils also released substantial CO₂ but did not show a strong trend in CO₂ and CH₄ release with water content. Knowledge of temporal and spatial variability in microbial C mineralization rates of Arctic soils in response to warming are key to constraining uncertainties in predictive climate models.

Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw

It has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments, and thus their stability and capacity to prevent carbon mobilization during permafrost thaw, is poorly understood. We have followed the dynamic interactions between iron and carbon using a space-for-time approach across a thaw gradient in Abisko (Sweden), where wetlands are expanding rapidly due to permafrost thaw. We show through bulk (selective extractions, EXAFS) and nanoscale analysis (correlative SEM and nanoSIMS) that organic carbon is bound to reactive Fe primarily in the transition between organic and mineral horizons in palsa underlain by intact permafrost (41.8 ± 10.8 mg carbon per g soil, 9.9 to 14.8% of total soil organic carbon). During permafrost thaw, water-logging and O₂ limitation lead to reducing conditions and an increase in abundance of Fe(III)-reducing bacteria which favor mineral dissolution and drive mobilization of both iron and carbon along the thaw gradient. By providing a terminal electron acceptor, this rusty carbon sink is effectively destroyed along the thaw gradient and cannot prevent carbon release with thaw.

Iron minerals trap carbon in permafrost, preventing microbial degradation and release to the atmosphere as CO₂, but the stability of this carbon as permafrost thaws is unclear. Here the authors use nanoscale analyses to show that thaw conditions stimulate Fe-reducing bacteria that trigger carbon release.

The thermal response of soil microbial methanogenesis decreases in magnitude with changing temperature

Microbial methanogenesis in anaerobic soils contributes greatly to global methane (CH₄) release, and understanding its response to temperature is fundamental to predicting the feedback between this potent greenhouse gas and climate change. A compensatory thermal response in microbial activity over time can reduce the response of respiratory carbon (C) release to temperature change, as shown for carbon dioxide (CO₂) in aerobic soils. However, whether microbial methanogenesis also shows a compensatory response to temperature change remains unknown. Here, we used anaerobic wetland soils from the Greater Khingan Range and the Tibetan Plateau to investigate how 160 days of experimental warming (+4°C) and cooling (−4°C) affect the thermal response of microbial CH₄ respiration and whether these responses correspond to changes in microbial community dynamics. The mass-specific CH₄ respiration rates of methanogens decreased with warming and increased with cooling, suggesting that microbial methanogenesis exhibited compensatory responses to temperature changes. Furthermore, changes in the species composition of methanogenic community under warming and cooling largely explained the compensatory response in the soils. The stimulatory effect of climate warming on soil microbe-driven CH₄ emissions may thus be smaller than that currently predicted, with important consequences for atmospheric CH₄ concentrations.

Soil microbes produce more methane as temperatures warm, but it is unclear if they acclimate to heat, or keep producing more of the greenhouse gas. Here the authors use artificial wetland warming experiments to show that after initial spikes in methane emissions after warming, emissions level out over time.

Comparative study on the pollution status of organochlorine pesticides (OCPs) and bacterial community diversity and structure between plastic shed and open-field soils from northern China

The pollution status of organochlorine pesticides (OCPs) and microbial community in plastic shed and open-field soils may be different due to the significant variations in environmental factors between the two cultivation modes. However, the differences remain unclear. We conducted a regional-scale survey to investigate the pollution level, distribution, and sources of 20 OCPs, and to evaluate the soil physicochemical properties and bacterial community in soils from plastic shed and open-field locating the north areas of China. We found that levels of total OCPs in the plastic shed soils were significantly higher than those in the nearby open-field soils. Most of these OCPs were attributed to historical application, except for dichlorodiphenyltrichloroethanes (DDTs) due to the fresh input along with dicofol application. Soil pH (for both cultivation modes) and total organic carbon (TOC) content (only for plastic sheds) were significantly correlated with the total OCP concentrations. Additionally, microbial diversity and richness were generally lower in plastic shed soils than in nearby open-field soils for each region. The bacterial community variation among different regions might be principally determined by the soil type. Soil pH had the greatest impact on the microbial community across all plastic shed and open-field samples. These results provide a better understanding of the environmental impact and ecological risk of OCPs in soils with different cultivation modes.

The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China

Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.

How did the bacterial community respond to the level of urbanization along the Yangtze River?

Bacterial communities in the sediment of the Yangtze River influenced by rapid urbanization have thus far been under-investigated despite the importance of microorganisms as mass transporters. Here, the response patterns of the bacterial community along the Yangtze River to different levels of urbanization were generated using 16S rRNA Miseq sequencing. The results reveal that economic aspects have made the largest contribution (41.8%) to the urbanization along the Yangtze River. A clear declining tendency in the abundance of Chloroflexi and Acidobacteria and a significant increase in the abundance of Bacteroidetes were observed with an elevated urbanization level gradient. Bacterial diversity showed a negative relevance (P < 0.01) to the demographic, economic and social urbanization index. Per capita gross domestic product (GDP) (PCGDP) and the GDP of tertiary industry (GDP3) exhibited significantly (P < 0.05) negative correlations with the bacterial diversity, while a positive relationship between the pH and α-diversity (P < 0.05) was observed. Redundancy analysis revealed that PCGDP was significantly correlated (13.9%, P < 0.01) with the overall bacterial compositions, followed by temperature (10.8%, P < 0.01) and GDP3 (8.4%, P < 0.05). Meanwhile, the GDP3 (35.9%), the ratio of total nitrogen and total phosphorus (N/P) (12.9%) and the PCGDP (8.8%) were revealed to be most significantly related to the metabolic bacteria (P < 0.05). The metabolic functions of the bacteria related to the N-cycle and S-cycle were significant in the sediment of the Yangtze River. The variations of the bacterial community and metabolic function responding to the rapid urbanization were related to the economic development via the influence of the 'mass effect'. In brief, the tertiary industry was significantly correlated with the variations in the composition of the metabolic community and the variations in the overall bacteria were both related to the tertiary and secondary industry.

Microbial diversity along a gradient in peatlands treating mining-affected waters

Peatlands are used for the purification of mining-affected waters in Northern Finland. In Northern climate, microorganisms in treatment peatlands (TPs) are affected by long and cold winters, but studies about those microorganisms are scarce. Thus, the bacterial, archaeal and fungal communities along gradients of mine water influence in two TPs were investigated. The TPs receive waters rich in contaminants, including arsenic (As), sulfate (SO42-) and nitrate (NO3-). Microbial diversity was high in both TPs, and microbial community composition differed between the studied TPs. Bacterial communities were dominated by Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria, archaeal communities were dominated by Methanomicrobia and the Candidate phylum Bathyarchaeota, and fungal communities were dominated by Ascomycota (Leotiomycetes, Dothideomycetes, Sordariomycetes). The functional potential of the bacterial and archaeal communities in TPs was predicted using PICRUSt. Sampling points affected by high concentrations of As showed higher relative abundance of predicted functions related to As resistance. Functions potentially involved in nitrogen and SO42- turnover in TPs were predicted for both TPs. The results obtained in this study indicate that (i) diverse microbial communities exist in Northern TPs, (ii) the functional potential of the peatland microorganisms is beneficial for contaminant removal in TPs and (iii) microorganisms in TPs are likely well-adapted to high contaminant concentrations as well as to the Northern climate.

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

Microbial diversity and biogeography in Arctic soils

Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO₂ , CH₄ and N₂ O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.

Biodiversity-function relationships in methanogenic communities

Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general, determines the rate of methane production is very limited. Studies to date have been correlational because of the difficulty in cultivating their constituent species in pure culture. Here, we investigate the causal link between methanogenesis and diversity in laboratory anaerobic digesters by experimentally manipulating the diversity of cultures by dilution and subsequent equilibration of biomass. This process necessarily leads to the loss of the rarer species from communities. We find a positive relationship between methane production and the number of taxa, with little evidence of functional saturation, suggesting that rare species play an important role in methane‐producing communities. No correlations were found between the initial composition and methane production across natural communities, but a positive relationship between species richness and methane production emerged following ecological selection imposed by the laboratory conditions. Our data suggest methanogenic communities show little functional redundancy, and hence, any loss of diversity—both natural and resulting from changes in propagation conditions during anaerobic digestion—is likely to reduce methane production.

Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments

Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH₄) and carbon dioxide (CO₂). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH₄production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.