Diversity Of Archaeal Communities Research Articles

Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. The archaeal and bacterial community diversity and structure were investigated through high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrolytic conductivity (EC) (arable 1 soil 2.3 dS m -1 and arable 2 soil 2.6 dS m -1 ) and a saline soil (EC = 17.6 dS m -1 ). The dominant bacterial phyla in the soils were Proteobacteria (relative abundance 46.2±8.9%), followed by Acidobacteria (13.1±9.1%) and Actinobacteria (10.0±4.8%), while Serratia (6.0±5.8%) and Bacillus (4.0±3.6%) were the dominant bacterial genera. Candidatus Nitrososphaera (53.5±46.8%) was the dominant archaeal phylotype in the arable soils, whereas Nitrosopumilus (0.4±0.01%) in the saline soil. The archaeal and bacterial community structure was different between the soils and the sand, As, Ba and Sb content had a significant effect on bacterial and archaeal community structure in the soils of this study, but not soil salinity.

Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid.

Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.

Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal and protist communities reveal niche divergences along environmental gradients in the Alps

Although widely used in ecology, comparative analyses of diversity and niche properties are still lacking for microorganisms, especially focusing on niche variations. Quantifying the niches of microbial taxa is necessary to then forecast how taxa and the communities they compose might respond to environmental changes. In this study, we first identified important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta diversity of bacterial, archaeal, fungal and protist communities. Then, we calculated the niche breadth and position of each taxon along the important environmental gradients to determine how these vary within and among the taxonomic groups. We found that edaphic properties were the most important drivers of both, community diversity and composition, for all microbial groups. Protists and bacteria presented the largest niche breadths on average, followed by archaea, with fungi displaying the smallest. Niche breadth generally decreased towards environmental extremes, especially along edaphic gradients, suggesting increased specialization of microbial taxa in highly selective environments. Overall, we showed that microorganisms have well defined niches, as do macro-organisms, likely driving part of the observed spatial patterns of community variations. Assessing niche variation more widely in microbial ecology should open new perspectives, especially to tackle global change effects on microbes.

Soil microbial communities are not altered by garlic mustard in recently invaded central Illinois forests

AbstractThe invasive forest plant garlic mustard (Alliaria petiolata) has been shown to alter soil microbial communities in the northeastern part of its invaded range in the United States, and this disruption of soil communities may contribute to its invasion success. However, garlic mustard allelochemistry can vary with invasion age, and it is not clear whether garlic mustard's impacts on soil microbes are consistent over its invaded range. Here, we compare the composition and diversity of soil fungal, bacterial, and archaeal communities among garlic mustard present, absent, and removed treatments in replicated blocks across five forests in the midwestern United States with relatively young garlic mustard invasions (approximately 17–26 years old, with consistent management). We collected samples in May and August, corresponding to garlic mustard active and senescent life history stages. While soil fungal and bacterial/archaeal communities (based on ITS2 region and 16S rRNA gene DNA sequencing, respectively) differed significantly between different blocks/forests and over time, we found no significant effect of garlic mustard treatment on soil microbial community composition or the relative abundance of mycorrhizal, saprotrophic, or pathogenic fungal guilds. The lack of garlic mustard impacts on the soil microbial community in recently invaded central Illinois forests suggests that these well‐documented impacts in the northeastern United States and in older invasions cannot necessarily be generalized across all environmental contexts.

Environmental Filtering by pH and Salinity Jointly Drives Prokaryotic Community Assembly in Coastal Wetland Sediments

Understanding the microbial community assembly is an essential topic in microbial ecology. Coastal wetlands are an important blue carbon sink, where microbes play a key role in biogeochemical cycling of nutrients and energy transformation. However, the drivers controlling the distribution patterns and assembly of bacterial and archaeal communities in coastal wetland are unclear. Here we examined the diversity, co-occurrence network, assembly processes and environmental drivers of bacterial and archaeal communities from inshore to offshore sediments by the sequencing of 16S rRNA gene amplicons. The value of α- and β-diversity of bacterial and archaeal communities generally did not change significantly (P> 0.05) between offshore sites, but changed significantly (P< 0.05) among inshore sites. Sediment pH and salinity showed significant effects on the diversity and keystone taxa of bacterial and archaeal communities. The bacterial and archaeal co-occurrence networks were inextricably linked with pH and salinity to formed the large network nodes, suggesting that they were the key factors to drive the prokaryotic community. We also identified that heterogeneous and homogeneous selection drove the bacterial and archaeal community assembly, while the two selections became weaker from offshore sites to inshore sites, suggesting that deterministic processes were more important in offshore sites. Overall, these results suggested that the environmental filtering of pH and salinity jointly governed the assembly of prokaryotic community in offshore sediments. This study advances our understanding of microbial community assembly in coastal wetland ecosystems.

Protein biomethanation: insight into the microbial nexus.

Biomethanation of carbohydrates (e.g., lignocellulosic biomass) and lipids (e.g., waste oils) has been well studied. However, investigations on the biomethanation of protein-rich biowastes (PRBs) and associated microbial communities have not been reported. This review summarizes the challenges in the metabolic process of anaerobic digestion of PRBs and the microbial instability associated with it. We discuss the diversity of bacterial and archaeal communities via metagenomics under PRB mono- and codigestion. A stable community structure with enhanced metabolic activity is a core factor in PRB biomethanation. The application of strategies such as codigestion of PRBs with carbon-rich biomass and microbial stimulation/augmentation would make PRB biomethanation more feasible.

First description of archaeal communities in carbonate-rich seafloor and subseafloor sediments from the Southwestern Atlantic slope

Deep-sea sediments comprise one of the largest habitats on Earth. The archaeal groups contribute to a large fraction of the deep-sea benthic biomass, playing a key role in biogeochemical cycles. However, their diversity in deep-sea benthic ecosystems remains poorly understood, mostly because only recently novel taxa have been proposed, thus remodeling the phylogenetic tree. Despite the dificulty in obtaining cultivated representatives, the metabolic capabilities of archaea have lately been described through metagenomic data, indicating that archaeal taxa are highly versatile. Here, we aimed to reveal the diversity of archaeal communities in surface (0 to 15 cm depth) and subsurface (200 cm depth) sediments from a carbonate-rich region in the Southwestern Atlantic upper slope. We performed 16S rRNA gene sequencing, and found that the archaeal composition in surface sediments was mainly dominated by ammonia-oxidizing archaea within Nitrososphaeria class. The distribution of Nitrososphaeria ASVs (amplicon sequence variants) indicates the presence of several species or ecotypes. Contrastingly, the subsurface sediment was dominated by uncultivated anaerobic and poorly known archaea, including representatives of all supergroups (Asgard, TACK, DPANN and Euryarchaeota). These archaea have been described as having potentially diverse metabolic capabilities, including autotrophic and heterotrophic pathways, such as acetogenesis, methylotrophy, and degradation of labile and recalcitrant organic compounds. This indicates an important role in the remineralization of organic matter in the SW (Southwest) Atlantic slope. They are likely enriched due to the transport and mixing of sediments by the IWBC (Intermediate Western Boundary Current) along the continental slope. However, further studies are needed to reveal the geochemical and oceanographic drivers of the archaeal distribution. This study provides the first description of the archaeal communities in carbonate-rich sediments in the SW Atlantic slope, and adds new biodiversity insights to this geological feature, which is considered a vulnerable marine ecosystem, thus helping for future conservation strategies.

Archaeal tetraether lipids and their biphytane carbon isotope composition in sediments along an estuarine biogeochemical gradient

The stable carbon isotopic composition of Thaumarchaeota-produced crenarchaeol (δ13Ccren) is thought to reflect the δ13C of dissolved inorganic carbon (DIC) and is valuable in carbon cycle research. Recently, an isotope flux-balance model was proposed that δ13Ccren is dependent on passive CO2 uptake and a slow rate of intracellular conversion to HCO3−, which has been validated in open ocean environments. However, further studies are required in environments with larger ranges of aqueous CO2 and diverse archaeal communities to examine whether the δ13Ccren value could still be predicted by the model. Here, we report δ13C values of biphytanes chemically released from the archaeal tetraether lipids (i.e., GDGTs) in sediments along a transect exhibiting shifts in the archaeal community and showing gradients of salinity, pH, and CO2 in the Pearl River Estuary, South China. Methanogenic and methanotrophic Euryarchaeota are present in the upper estuary, although not significant, as revealed by the elevated relative abundances of GDGT-0 and higher values of methane index in suspended particulate matter (SPM) and surface sediments, as well as the more 13C-depleted C40:0, C40:1, and C40:2 biphytanes than the C40:3 biphytane released from sedimentary GDGTs. Toward the lower estuary and coastal sea, GDGT distributions in SPM and sediments tend to indicate archaeal communities under normal marine conditions. However, there are still differences in δ13C values between C40:0 and C40:3 biphytanes by up to 2.4‰ in sediments, although C40:1, C40:2, and C40:3 were similar in δ13C, likely due to the existence of marine group II Euryarchaeota. Along such a physicochemical and biogeochemical gradient, the values of sedimentary δ13C40:3 increase monotonically with the increase of mean annual pH and the decrease of mean annual CO2. This phenomenon resembles the reported δ13CGDGT profiles, along with the variations in pH and CO2, in water column in the open ocean, and hence consistent in direction with the isotope flux-balance model for Thaumarchaeota lipids. However, our estimated apparent biosynthetic isotope effect (εAr) of crenarchaeol, ranging from 15.2‰ to 19.7‰, is mostly lower than those estimated in the open ocean. With the constraints of thaumarchaeal growth rates in such a dynamic estuarine environment as well as those in the open ocean, we suggest slight reductions in catalytic efficiency and intracellular kinetic isotope effect of intracellular CO2 hydration relative to previously employed values. Such modifications would slightly change the sensitivities of εAr to archaeal growth rate and ambient CO2 concentration but might be more suitable for variable hydrology and community environments.

The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition, and functions

Nitrapyrin is a nitrification inhibitor used to retain ammonia-N in soil to improve crop yields and quality. Nitrapyrin targets specifically the ammonia oxidizers, but it is not known if it has non-target effects on the soil microbial communities. Here, we tested the hypothesis that nitrapyrin also leads to large shifts in soil microbial community structure, composition, diversity and functions. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice (at grain filling and harvest), the 16S rRNA gene and ITS region were amplified and sequenced to follow the changes in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR, and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. Sampling dates and soil compartments had overwhelming effects on the microbial communities. However, nitrapyrin still significantly affected the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with the sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling dates significantly influenced the profiles observed. Our results show that nitrapyrin influences non-target soil- and plant-associated microbial communities. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.

House fly larval grazing alters dairy cattle manure microbial communities

BackgroundHouse fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae.ResultsBacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities.ConclusionsHouse fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.

Effects of buffelgrass removal and nitrogen addition on soil microbial communities during an extreme drought in the Sonoran Desert

Buffelgrass (Cenchrus ciliaris), an invasive perennial grass in arid regions of the United States, has drastically modified natural ecosystems. Understanding the aboveground–belowground links between buffelgrass invasion and soil microbial communities will be critical for developing a comprehensive understanding of arid ecosystems and for deploying successful control strategies. In a randomized block‐field experiment located in Tucson, AZ, U.S.A., we investigated the effects of buffelgrass removal via hand pulling and nitrogen addition (and their interaction) on soil microbial communities during an extreme drought (summer 2020). We found that experimental treatments did not significantly impact bacterial and archaeal community diversity and composition, while plant removal affected fungal community diversity and composition. In addition, the removal treatment increased the proportion of putative chitinolytic bacteria (genus Lysobacter) and decreased the proportion of putative fungal endophytes (genus Darksidea). Buffelgrass manual removal appeared to favor fungal endophyte death around and inside of leftover intact roots, which may result in an increase of chitinolytic bacteria thriving on the degradation of fungal cell walls. Overall, our results suggest that hand removal—which is a common type of buffelgrass control—can alter soil fungal communities and the proportion of certain microbial functional groups. As these changes could subsequently affect native plants, more research is needed to develop a comprehensive understanding of the effect of buffelgrass control efforts on target plants as well as surrounding ecosystem dynamics.

Variability of Microbial Community Structure Distribution in Marine Shallow Surface Sediments in Shenhu Area

Due to the frequent exchange of matter and energy between living and non-living matter in seawater, the surface layer, particularly the distribution of microorganisms in centimeter-scale and element concentrations in surface sediments, demonstrates the important message of the local biogeochemical environment. This work probed the differences in microbial communities between two sampling cores obtained from the same area and the possible environmental factors, e.g., in situ component and concentration in porewater. Here, high-throughput sequencing (16S rRNA, Illumina sequencing) and quantitative PCR analysis were used to investigate the diversity of microorganisms in sediments of two push cores of L1 and S8 from Shenhu Area, South China Sea. Porewater concentration of components and isotopic fractionation were also obtained to explore the possible correlation between the microbial community and the chemical compositions of porewater. Q-PCR revealed bacteria play an important role in the geochemical cycle in the surface sediments, and archaea may be the main community in response to environmental changes and maintain the local marine ecosystem. The total gene copies of microorganisms in the study area were lower than nearby marine sediments. Microbial community compositions showed the dominant microbial phyla were similar on Phylum level in L1 and S8, with only different abundances. Firmicutes and Proteobacter were the main bacterial phyla, while Thaumarchaeota, Lokiarchaeota and Bathyarchaeota dominated the archaeal community. The abundance of the dominant class varied significantly between L1 and S8. Bacilli in Firmicutes and Gammaproteobacteria in Proteobacter were prevalent bacterial class, MGI in Thaumarchaeota was the predominant archaeal class in L1, while Thermoplasmata and Group-C3 dominated in S8. PCoA results showed a clear diversity of bacterial and archaeal communities between these two sites, as well as significant geographic variation in microbial communities. RDA results revealed that a complex combination of environmental factors might correlate to microbial communities in a marine dynamic environment. Here, δ13CDIC, DIC and SO4 2– were strongly correlated to the bacterial communities, whereas δ13CDIC, Fe2+ and SO4 2– concentration linked to archaeal communities. Microbial communities and RDA results suggested carbon may be the main factor related to the microbial community in L1, while Fe2+ correlated with microbial community composition in S8. SO4 2– concentration and the distribution of Gammaproteobacteria indicated that the sulfur cycle is probably active in this area.

Subsoiling and conversion to conservation tillage enriched nitrogen cycling bacterial communities in sandy soils under long-term maize monoculture

Desertification degrades soil health and severely reduces crop productivity. Conventional tillage practices can amplify these problems in arid and semi-arid regions. For semi-arid regions in Inner Mongolia, China, the effects of introducing different tillage practices such as subsoiling (SS), straw mulching (SM), and no-tillage (NT) on otherwise long-term conventional tilled maize monoculture systems, were examined in the context of sandy soil bacterial and archaeal community diversity. Results showed that after three to four years of introduction, subsoiling and conversion to conservation tillage practices had no immediate effect on the alpha-diversity of the soil microbial communities. The beta-diversity of the soil microbial communities was less affected by the introduced tillage practices than by the growing season conditions, soil moisture, total nitrogen, soil macro-aggregate, and organic matter. Importantly, the introduced tillage practices had a notable effect on soil microbial communities associated with nitrogen (N) cycling processes, especially N fixation, nitrate reduction, nitrification, and denitrification. In particular, several years of tillage change from long-term conventional tillage enhanced the abundance of KEGG orthologs (KOs) associated with N fixation function involving species in Rhodoplanes, Nitrospira, Skermanella, and Rhizobium according to PICURSt prediction. Rhodoplanes spp. are involved in nitrate reduction and denitrification processes, and Nitrospira spp. associated with nitrite oxidization. We conclude that, for maize monoculture systems in semi-arid sandy soils, the soil bacterial and archaeal communities associated with many beneficial N cycling processes can be significantly impacted by only three to four years of introduced conservation and subsoiling tillage practices.

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.

Effects of Fe3O4 nanoparticles on anaerobic digestion enzymes and microbial community of sludge

ABSTRACT Fe3O4 nanoparticles (NPs) have potential effects on the anaerobic digestion of excess sludge. The effects of different concentrations of Fe3O4 NPs (0, 100, 200, 400 and 600 mg/L) on enzymes and microorganisms in anaerobic digestion were studied to explore the mechanism of the effect of Fe3O4 NPs on anaerobic digestion. The results showed that 100, 200 and 400 mg/L Fe3O4 NPs could promote anaerobic digestion, and 200 mg/L Fe3O4 NPs had the most obvious promoting effect. The activities of protease, cellulase, dehydrogenase, acetic kinase and coenzyme F420 in the 200 mg/L Fe3O4 NPs group reached 120 U/mg VS, 71.75 U/g VS, 135 U/mL, 94 mol/L, 1.37 umol/g VSS, respectively, which were 3.8, 1.5, 1.2, 1.2 and 1.6 times of the blank group, respectively. However, when the concentration of Fe3O4 NPs reached 600 mg/L, the activities of cellulase, dehydrogenase and acetic kinase were lower than those of the blank group, and anaerobic digestion was inhibited. The above conclusions can also be confirmed by high-throughput sequencing. The abundance of longilinea and ornatilina in the 200 mg/L Fe3O4 NPs group was 8.8% and 4.1% respectively, and methanthrix abundance was 69%, which was more conducive to decomposition acetic acid into CH4.

The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.

Simple SummaryArchaea is identified as the key link in the interaction between gut microbiota and host metabo-lism. Studies on human and mice have reported archaea, especially methanogenic archaea, makes an important impact on the energy harvesting capacity of the host by improving fermentation. But, in pigs, the metabolic potential of archaea at different production stages are still largely unknown. Herein, we re-analyzed 276 metagenomic samples to explore the diversity, composi-tion, and potential functions of archaea in pigs. The results showed significant regional variations in archaeal composition. Furthermore, the Metacyc pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, and archaea may be involved in carbohydrate metabolism and de novo synthesis of some kinds of essential amino acid. Overall, metagenomic re-analysis revealed that the composition and functional potential of archaea in the swine gut and suggested that archaea may make an important function in pigs.Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

Cropland‐to‐Miscanthus conversion alters soil bacterial and archaeal communities influencing N‐cycle in Northern China

AbstractMiscanthus spp. are increasingly cultivated in cropland worldwide due to their bioenergy potential and multiple ecological services. Effects of long‐term cropland‐to‐Miscanthus conversion without N fertilizer on soil microbiome and N cycling largely remain unknown. We aimed to explore the effects of Miscanthus conversion on soil microbiome and N cycling over a 15‐year period. We analyzed diversity, composition, and abundance of bacterial and archaeal communities using 16S rRNA amplicon sequencing, and abundances of N‐cycling‐related genes using quantitative polymerase chain reaction of 0–10 cm soils collected from bare land, cropland, 10‐year Miscanthus × giganteus, and 15‐year Miscanthus sacchriflorus land in Beijing. Conversion decreased soil sand and micro‐aggregate proportion, nitrate N (NiN), available phosphorus levels, conductivity, temperature, and pH, while increasing proportion of soil clay and macro‐aggregate (MAA), soil organic C (SOC), available N (AN), exchangeable Mg2+ (EMg2+), and available potassium (AK) contents as well as microbial C/N. Consequently, diversity, composition, and abundance of soil bacterial community exhibited larger changes than those values of archaeal community after conversion. Soil AP, EMg2+, AK, and SOC were key factors in shifting microbiome from the cropland to Miscanthus pattern. Moreover, abundances of bacterial and archaeal communities and the N fixer gene nifH increased, whereas that of the bacterial ammonia monooxygenase gene decreased. The copies of other N‐cycling‐related genes in the two Miscanthus lands seemed similar to those values of cropland. The nifH copies negatively correlated with soil NiN and positively correlated with AN, EMg2+, ECa2+, SOC, AK, and MAA. We conclude that changes in soil microbiome pattern induced by the variation of soil properties enhance microbial N fixation potential, maintaining stable N levels and robust N cycling with lower N leakage risk after conversion. These results should inspire farmers and governments to large‐scale use Miscanthus on marginal cropland in Northern China.

Variations in the diversity of soil bacterial and archaeal communities in response to different long-term fertilization regimes in maize fields

Understanding the effect of different agricultural practices on soil microbiome is very important since it has a decisive role in the multifunctionality of soils. Our research aimed to reveal and compare the changes in the composition of soil bacterial and archaeal communities in response to cultivation and fertilization regimes. Soil samples were collected from a long-term (60-year-old) field experiment with maize (Zea mays L.) monoculture under inorganic fertilization, combined fertilization (inorganic and farmyard manure) and without fertilization, and a nearby fallow land five times over a crop cycle. The bacterial and archaeal community compositions were revealed by amplicon sequencing of the 16S rRNA genes on Illumina MiSeq platform. Significant differences were observed between cultivated soils and fallow land, as well as among cultivated soils under different fertilization regimes in both bacterial and archaeal community structures. Many taxa (e.g. Gaiella, Burkholderiaceae, Saprospiraceae, Rhodoplanes, MB-A2-108 and Cand. Nitrososphaera) were found to be more abundant in the fallow land than in the cultivated soils. The exclusive use of inorganic fertilizer resulted in a significantly different bacterial and archaeal community structure with higher relative abundance of sequences affiliated with mostly acidotolerant taxa (e.g. Bryobacter, Cand. Solibacter, Acidibacteriales, WPS-2 and Cand. Nitrosotalea). These taxa were not enriched in the combined fertilizer treatment, even though the manure was applied only once every four years. The results demonstrated a strong effect of inorganic fertilizers on the soil bacterial and archaeal communities, however, these effects can be decreased by the application of farmyard manure.

Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China.

The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.

The impact of reduced graphene oxide (rGO) supplementation on cattle manure anaerobic digestion: Focusing on process performance and microbial syntrophy

At a time when there is a surge in demand for increasing renewable energy production, boosting biomethane production per unit organic matter/waste has become a big challenge and necessity. In this study, the effect of rGO addition on biomethane production from cow manure under mesophilic-batch conditions was investigated. Biomethane production was increased via rGO supplementation at appropriate concentrations. The highest biomethane production, which was 335 mL/gVSad (65 % increase), was obtained by adding 20 mg/L rGO (CM20) while rGO addition slightly increased (up to 5.4 %) the CH4 content of biogas. The microbial community analysis indicated that via rGO supplementation, the dominant bacteria changed from Levilinea to Candidatus Cloacamonas and a more diverse archaeal community was formed. According to this study results, rGO supplementation could be used at biogas plants to boost renewable energy production.