Archaeal Community Composition Research Articles

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte.

Marine sponges are abundant and ecologically important components of coral reefs and have been shown to harbour exceptionally high microbial densities, which can differ substantially among sponge species. However, this dichotomy between high and low microbial abundance (HMA, LMA) sponges is still not fully understood, particularly as concerns the archaeal community. This study aims to fill this gap by analysing (using 454-pyrosequencing of the 16S rRNA gene) how the archaeal community varies among known LMA (Stylissa carteri, and Stylissa massa), known HMA (Hyrtios erectus and Xestospongia testudinaria) and unknown HMA/LMA status sponge species (Ectyoplasia coccinea, Paratetilla bacca and Petrosia aff. spheroida) collected in a remote location in which very few sponge microbial composition studies have been previously performed (Mayotte, Comores archipelago, France) and comparing the results with those reported in four other geographical areas. Based on archaeal community composition, the known LMA sponges formed a distinct cluster together with Paratetilla bacca, Ectyoplasia coccinea and seawater while the known HMA sponge X. testudinaria formed a cluster with Petrosia aff. spheroida. The known HMA sponge H. erectus, in turn, had an intermediate archaeal community between HMA sponges and sediment samples. In addition to the above, we also showed significant compositional congruence between archaeal and bacterial communities sampled from the same sponge individuals. HMA sponges were mainly dominated by members assigned to the genus Nitrosopumilus while LMA sponges were mainly dominated by members assigned to the genus Cenarchaeum. In general, there was no clear difference in richness between HMA and LMA sponges. Evenness, however, was higher in HMA than LMA sponges. Whilst the present study corroborates some of the traits commonly associated with the HMA-LMA dichotomy (higher evenness in Mayotte HMA sponges), this was not consistent across geographical areas showing that more research is needed to fully understand the HMA/LMA dichotomy as concerns Archaea.

247 The effect of diet on the microbial community structure and composition in lactating Jersey cows consuming a mixture of straw and dry distillers grains plus solubles in replacement of alfalfa hay

Abstract The rumen microbial community is responsible for producing a majority of the energetic needs for the animal, yet our understanding of the rumen microbiome is in its infancy. To better understand the effect of corn-ethanol coproducts on rumen microbial communities, a replicated 4 × 4 Latin square design study utilizing 12 cows in three squares was conducted to evaluate the replacement of alfalfa hay with a mixture (CoP) containing straw and dried distillers grains plus solubles (DDGS) in lactating Jersey cows. The experimental treatments were (proportions on a dry matter basis): a control diet (CON) containing 18.2% of alfalfa hay with no straw or DDGS. A low coproduct diet (LCoP) containing 12.1% alfalfa, 2.1% straw, and 6.0% DDGS. A medium coproduct diet (MCoP) containing 6.1% alfalfa, 4.2% straw, and 12.1% DDGS. A high coproduct diet (HCoP) containing 6.2% straw, 18.1% DDGS with no alfalfa. Rumen digesta samples were collected via an esophageal tube. No differences were observed for milk production and dry matter intake (P ≥ 0.307) (mean ± SEM) 19.5 kg ± 0.60, 29.6 kg ± 0.91, across treatments, while a decrease in methane was observed (P < 0.01) for the HCoP treatment. The bacterial community was assessed by sequencing the V4 region of the 16S rRNA gene. Additionally, the archaeal community was assessed by sequencing the V4-V5 region of the 16S rRNA gene on the Illumina MiSeq platform. Amplicon Sequence Variants were identified using the DADA2 pipeline. No significant differences were observed for the bacterial (P = 0.334) and archaeal (P = 0.593) communities. Although global effects in microbial community dynamics were not observed, differential taxa were observed with Lachnospiraceae being the major differentially abundant Family. The archaeal community composition demonstrated that Methanobacteriales to be the differentially abundant Order across treatments, and may contribute to methane production.

Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition

Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD5) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.

Elucidating the archaeal community and functional potential in two typical coastal wetlands with different stress patterns

Archaea play dominant roles in nutrient cycling, but the archaeal community and function in coastal wetlands with different stress patterns remain poorly understood. Here, two typical coastal wetlands of the Yellow River estuary, Zone A with only tidal erosion and Zone B with runoff and tidal invasion, were selected to explore the possible differences in archaeal community and function and evaluate the influential factors. Compared with Zone B, Zone A had higher levels of total nitrogen, available phosphorous (AP) and pH. Thaumarchaeota was the most abundant archaeal phylum, followed by Euryarchaeota in Zones A and B. Candidatus_Nitrosopelagicus (30.85% in Zone A, 36.04% in Zone B) and Candidatus_Nitrosopumilus (24.10% in Zone A, 39.01% in Zone B) were the dominant ammonia-oxidizing archaea in both zones, and Haloarcula and Haloferax were the dominant denitrifying halophilic archaea in Zone A. Organisms from methanogenic genera Methanobrevibacter, Methanocorpusculum and Methanosarcina were enriched in Zone A. Anaerobic methanotrophic Candidatus_Methanoperedens (ANME-2d) had relatively low abundance in Zones A and B. These archaea were the key factors in maintaining the carbon and nitrogen cycles in coastal wetlands. Moreover, nitrification was relatively active in Zone B, and denitrification and methanogenesis dominated in Zone A. Redundancy analysis revealed that AP, NH4+–N, pH, salinity and moisture played important roles in the determination of archaeal community composition at the genus level. Microbial community and PICRUSt analysis indicated that the archaeal communities changed significantly, but the functions were relatively stable for both zones. This finding suggests that environmental selection in similar habitats could lead to functional convergence. The relative gene abundances of nitrate reductase were relatively high, indicating that aside from denitrification, a large amount of nitrite as an electron acceptor was present to perform nitrite-driven anaerobic methane oxidation via reverse methanogenesis. The findings help in understanding the impacts of different stress patterns on archaeal community composition and functional potential in coastal wetlands.

Differential response of microbial diversity and abundance to hydrological residual time and age in cascade reservoirs

Freshwater sediments harbor taxonomically and metabolically diverse microbial communities, which play critical roles in aquatic ecosystems. However, little is known about the biogeographical patterns of assembly of such sedimentary communities, especially in cascade reservoirs of various age and hydrological characteristics. Using Illumina sequencing and quantitative real-time polymerase chain reaction targeting the 16S rRNA gene, we investigated spatial patterns of both bacteria and archaeal communities across eight reservoirs (including Hongfeng Reservoir (HFy), Hongjiadu Reservoir (HJDy), Wujiangdu Reservoir (WJDs), Dongfeng Reservoir (DFs), Silin Reservoir (SLd), Pengshui Reservoir (PSd), Suofengying Reservoir (SFYd), and Yinpan Reservoir (YPd)), forming the largest cascade reservoir system located on the Wujiang River, the tributary of the upper Yangtze River. Longer hydrological residual times promoted the proliferation of bacteria while reducing their diversity. In structures of different age, distinct archaeal communities were observed, with more abundant and diverse archaea in the earlier constructed reservoirs (HFy, WJDs). Both environmental factors (redundancy analysis) and spatial scale (non-metric multidimensional scaling analysis) determined community structures. The abundances of bacteria and archaea were both positively correlated with the presence of nutrients. In particular, a shift in the composition of the sedimentary archaeal community was observed along with increasing trophic complexity of these reservoirs, from Thaumarchaeota- towards Euryarchaeota-dominated communities. Also, the preference of several phyla of bacteria, including Latescibacteria and Bacteroidetes, for anaerobic and eutrophic habitats was significantly positively correlated with the presence of nutrients in these reservoirs. We demonstrated the existence of different distribution patterns of bacterial and archaeal communities in reservoir sediments, reflecting both deterministic and stochastic processes distinctly regulating the abundance of bacteria and archaea, in response to hydrological and biogeochemical changes after water impoundment in cascade reservoirs along a large river.

Anaerobic bioconversion efficiency of rice straw in continuously stirred tank reactor systems applying longer hydraulic retention time and higher load: One-stage vs. Two-stage

This study investigated the anaerobic bioconversion efficiency of rice straw in continuously stirred tank reactor (CSTR) applying longer hydraulic retention time (HRT) and higher load. Two HRT distributions and two loads were studied and compared for one-stage and two-stage CSTR systems. The results indicated that the two system with longer HRT (60d) and higher load (160g TS·L−1) obtained 11.06% and 14.28%, 15.24% and 19.38%, more biogas and methane productions than those of one-stage system with HRT (50d) and load (140g TS·L−1), respectively, while maintained stable operation at higher loads. It was also found that the microbial richness, diversity, and bacterial and archaeal community compositions showed some differences between two systems with different HRTs and loads, which was thought to be one of reasons leading to the differences in bioconversion efficiencies. The study indicated that two-stage system applying longer HRT and higher load could be one of the effective methods for more bioenergy recovery from rice straw.

Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake

The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria, Nitrospirae, Chloroflexi, Firmicutes and Ignavibacteriae. The dominant groups of archaea consisted of Euryarchaeota, Woesearchaeota DHVEG-6, Bathyarchaeota and WSA2. Lastly, the meta-analysis results highlighted that the low TOC (LT) prokaryotic community structure is larger and more complex compared to moderate TOC (MT). On the whole, the prokaryotic community structure is obviously distinct among groups with different TOC levels, and LT communities may interact with each other strongly in the Dianchi Lake sediment. This study can provide more insights into prokaryotic assemblages in eutrophic lake sediment and provide suggestions for the restoration and maintenance of sediment ecosystems.

Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone.

Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.

Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil

Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community’s resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis.

BackgroundThe architecturally important coral species Acropora cervicornis and A. palmata were historically common in the Caribbean, but have declined precipitously since the early 1980s. Substantial resources are currently being dedicated to coral gardening and the subsequent outplanting of asexually reproduced colonies of Acropora, activities that provide abundant biomass for both restoration efforts and for experimental studies to better understand the ecology of these critically endangered coral species.MethodsWe characterized the bacterial and archaeal community composition of A. cervicornis corals in a Caribbean nursery to determine the heterogeneity of the microbiome within and among colonies. Samples were taken from three distinct locations (basal branch, intermediate branch, and branch tip) from colonies of three different coral genotypes.ResultsOverall, microbial community composition was similar among colonies due to high relative abundances of the Rickettsiales genus MD3-55 (Candidatus Aquarickettsia) in nearly all samples. While microbial communities were not different among locations within the same colony, they were significantly different between coral genotypes. These findings suggest that sampling from any one location on a coral host is likely to provide a representative sample of the microbial community for the entire colony. Our results also suggest that subtle differences in microbiome composition may be influenced by the coral host, where different coral genotypes host slightly different microbiomes. Finally, this study provides baseline data for future studies seeking to understand the microbiome of nursery-reared A. cervicornis and its roles in coral health, adaptability, and resilience.

The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories.

SummaryWe explore archaeal distributions in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, México. Sampling locations include (1) control sediments without hydrothermal or seep influence, (2) Sonora Margin sediments underlying oxygen minimum zone water, (3) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (4) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal communities largely comprise Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. Variations in archaeal community composition reflect locally specific environmental challenges. Background sediments are divided into surface and subsurface niches. Overall, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin and Sonora Margin sediments.

Long-term chemical fertilization-driving changes in soil autotrophic microbial community depresses soil CO2 fixation in a Mollisol

Soil is the largest C pool in the terrestrial ecosystem. Numerous studies have been devoted to the decomposition of soil organic C as influenced by agricultural management. However, little is known about the effect of fertilization on the microbial CO2 fixation potential. Here, we examined the atmospheric CO2 fixation rates and structure of autotrophic cbbL-containing bacterial communities and accA-containing archaeal communities in response to 38 years of chemical and/or organic fertilizer application in a Mollisol. The autotrophic microbial abundance and community composition were analyzed by quantitative polymerase chain reaction and high throughput sequencing, respectively. Our results showed that chemical fertilization additions significantly decreased CO2 fixation rates by 57%, but organic manure use resulted in no notable differences compared to no fertilizer regimes (0.38 mg CO2 kg−1 soil d−1) through stable isotope methods. The declining soil pH and increasing Olsen-phosphorus in soils with chemical fertilization dramatically reduced the cbbL gene diversity and accA gene abundances and altered both the autotrophic bacterial and archaeal community compositions. The changes in CO2-fixation rate were more greatly attributed to the shifts in autotrophic bacterial community composition than to the diversity and abundance. The C fixation potentials were positively correlated with the relative abundances of Acidiphilium and Methylibium but were negatively related to those of Azospirillum and Nitrosospira. Both composition and abundance of the autotrophic archaeal community contributed together to the CO2 fixation activities. Our finding suggests that long-term chemical fertilization has a strong impact on the soil microbial CO2 fixation activity and autotrophic microorganisms in upland soils and highlight the important roles of the CO2 fixing process in soil organic carbon sequestration.

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida).

Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.

Intact Ether Lipids in Trench Sediments Related to Archaeal Community and Environmental Conditions in the Deepest Ocean

AbstractArchaea play an important role in marine biogeochemical cycle; however, their phylogenetic distribution and lipid composition in the hadal zone (6–11 km water depth) are poorly known. Here, we analyzed archaeal membrane lipids and 16S rRNA gene sequences in sediments from Mariana Trench (MT), Massau Trench (MS), and New Britain Trench (NBT), varying from 1,560 to 10,840 m depth. Forty‐two intact polar lipids (IPLs) were identified, including glycerol dialkyl glycerol tetraethers (GDGTs), OH‐GDGTs, glycerol dialkyl diethers (GDDs), and archaeol (AR) with polar headgroups of monohexose (1G), dihexose (2G), trihexose (3G), and hexose‐phosphohexose (HPH). Compositional and spatial distribution patterns of archaeal lipids suggest benthic Thaumarchaeota as a major source for IPLs, consistent with the predominance of Thaumarchaeota genes (&gt;80%). The redundancy analysis (RDA) based on lipid and 16S rRNA data separates samples into three groups: extremely deep water (MT), significant terrestrial influence (NBT 1, 4, and 6), and predominant marine influence (MS, NBT 2, 3, 7, and 10). 1G‐GDDs and 1G‐AR positively correlate with water depth, likely reflecting the adaptation of benthic archaea to elevated hydrostatic pressure or variation of archaeal community in trench sediments. Bathyarchaeota are more abundant in sediments receiving terrestrial input; this pattern was attributed to their capability of utilizing terrestrial organic matter as an energy source. Our study highlights important environmental influences (e.g., pressure and organic matter quality and quantity) on benthic archaeal community and archaeal IPL compositions, which should be considered when IPLs and core lipids are applied as chemotaxonomic markers and paleo‐proxies.

Microbial diversity of two natural CO2-rich springs with contrasting hydrochemical features

Microbial communities in CO2-rich springs have adapted to environmental pressure including low pH resulting from high concentrations of CO2. Microbial community composition and hydrochemical characteristics in the CO2-rich springs are important features affected by high levels of CO2 in groundwater ecosystems, and they may be useful indicators of CO2 leakage from carbon capture and storage (CCS) sites where CO2 is injected into deep geological reservoirs for the mitigation of climate change. To determine how long-term CO2 leakage affects the groundwater ecosystems, we analyzed the bacterial and archaeal community composition and hydrochemical features of two different natural CO2-rich springs, Hansil (HS) and Chosukol (CS), located in south-eastern Korea which are natural analog sites for groundwater ecosystems affected by CO2 leakage from geological CO2 storage sites. Analyses of hydrochemical characteristics and 16S rRNA gene amplicon sequencing of bacteria and archaea revealed a marked distinction between the two springs. The pH, the concentrations of bicarbonate ion (HCO3-), major cations including Ca2+ and Mg2+, and specific trace elements including Fe and Mn were higher in HS as compared to CS while no distinction in pCO2 between the two springs was observed. Microbial community composition was distinct between the two springs at the genus level. Specifically, the relative abundance of Gallionella, an iron-oxidizer, was significantly higher in HS whereas that of Albidiferax known as dissimilatory iron-reducing bacteria was higher in CS than HS, reflecting the difference of iron concentration in the two springs. In our study, microbial community composition appeared to be more strongly affected by the concentration of iron than that of CO2. Our results enhance the understanding of hydrochemical features and microbial communities in natural CO2-rich springs and suggest that microbial communities may be useful indicators of CO2 leakage from CCS sites.

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.

Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management

Strategic tillage (ST) has been proposed to help control weeds that germinate during fallow-periods in continuous no till (NT) farming systems, but its effects on soil biological properties are unclear. ST is a type of reduced tillage (RT) that places particular emphasis during the decision-making process on agro-climatic conditions, and the frequency, timing and implements used to till. Here, we assessed the impacts of one-time ST following 44 years of continuous NT or conventional tillage (CT) on soil microbial diversity, biomass, enzymatic activity and substrate utilisation potential at two depths. The composition of bacterial and archaeal communities differed significantly between contrasting land management (CT vs NT); albeit albeit no differences were observed after ST. Meanwhile, fungal community composition was not affected by contrasting land management or ST. Biological indicators for catabolic diversity, microbial biomass and enzymatic activity showed no significant changes after ST operation. Our results suggest that, in the short-term (13 months), ST exerts only minor impacts on a range of biological properties, as well as, bacterial, archaeal and fungal diversity. Hence, ST has the potential to be used as a strategy to control weeds and diseases without compromising soil health.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources

Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.

The Saltpan Microbiome is Structured by Sediment Depth and Minimally Influenced by Variable Hydration.

Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.

Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA.

Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.