Archaeal Community Composition Research Articles

Evolution characteristics and molecular constraints of microbial communities during coal biogasification.

This study investigates the production of biomethane, and variation in microbial community and coal molecular structures using gas chromatography, 16S rRNA high-throughput sequencing and Fourier transform infrared spectroscopy. Additionally, the factors influencing microbial community structure at a molecular level are discussed. The results demonstrate that bituminous coal exhibits a higher biomethane yield than anthracite coal. In bituminous coal samples, Escherichia and Proteiniphilum are the predominant bacteria at day 0, while Macellibacteroides dominates from days 5 to 35. Methanofollis is the dominated archaea during days 0 to 15, followed by Methanosarcina on day 35. In anthracite coal samples, Soehngenia is the dominant bacterial genus at day 0; however, it transitions to mainly Soehngenia and Aminobacterium within days 5-15 before evolving into Acetomicrobium on day 35. Methanocorpusculum is predominantly found in archaeal communities during days 0-15 but shifts to Methanosarcina on day 35. Alpha diversity analysis reveals that bacterial communities have higher species abundance and diversity compared to archaeal communities. Redundancy analysis indicates a significant correlation between coal molecular structure and bacterial community composition (P value < 0.05), whereas no correlation exists with archaeal community composition (P value > 0.05). The research findings provide theoretical support for revealing the biological gasification mechanisms of coal.

Enhancing methane yield and shifting microbial communities in anaerobic reactors treating lipid-rich dairy wastewater through exogenous lipase addition

This study explores a novel enzymatic pretreatment approach in anaerobic reactors for dairy wastewater, using lipase AY Amano to enhance methane production and modify microbial and archaeal community composition. Batch and semi-batch reactors with a total volume of 2000 mL were used to treat dairy wastewater with initial COD of 2000 and 15,000 mg L−1, respectively. In a new novel approach, the semi-batch reactors underwent a three-phase operation: 30 days of acclimation, 30 days of rest, and 30 days of active operation. Adding lipase (0.05% wv−1) as a pretreatment significantly increased methane yield over the 90 days by 135–138% compared with the control (without enzyme addition). The organic loading rate reached 0.22 g COD day−1 L−1. Furthermore, 30 days after the end of the semi-batch reactor approach (120 days from the start), reusing sludge in batch reactors increased methane yield by 114–122% compared to the control. This increase was linked to the emergence and shift of new methanogenic communities within the sludge. Integrating hydrolytic enzymes into the anaerobic treatment enhances performance and sustainability by fostering methanogen-enriched microbial communities. This is crucial for maximizing methane production but may increase costs, requiring further economic feasibility research.

Archaeal communities in natural and artificially restored mangrove sediments in Tieshan Bay, China

Mangrove forests are crucial wetland ecosystems located in tropical and subtropical intertidal zones, but they have become extensively degraded. As a viable ecological restoration strategy, the cultivation of native mangrove vegetation in these degraded areas has gained considerable attention. Mangroves’ unique environmental conditions make them suitable habitats for diverse microbial communities, including Archaea - one of the main microbial communities in mangrove sediments - which plays a pivotal role in biogeochemical cycles. However, little is known about the dynamics of archaeal communities during mangrove restoration through phytoremediation. In this study, we investigated the physicochemical properties of sediment profiles from natural and artificially restored mangrove ecosystems in Tieshan Bay. We utilized quantitative polymerase chain reaction (qPCR) and 16S rRNA gene sequencing techniques to explore differences in abundance, community structure, and composition of archaeal communities between sediment profiles in natural and artificially restored mangrove ecosystems. We also examined correlations between archaeal communities and environmental factors. Our results revealed that Crenarchaeota, Thermoplasmatota, Asgardarchaeota, Nanoarchaeota, and Euryarchaeota were the predominant archaeal phyla, with significant variation in sediment composition observed for Crenarchaeota and Thermoplasmatota in different depths. We also found significant differences in archaeal abundance and community composition between natural and restored mangrove sediments. Furthermore, C/N ratio and pH emerged as primary drivers of archaeal communities in wet and dry season sediments, respectively. Additionally, the study revealed seasonal disparities in seasonal differences in the relative abundance of certain archaeal groups (such as Asgardarchaeota, Nanoarchaeota). Network analysis demonstrated stronger interconnections among archaeal communities in sediments from natural mangroves than from artificially restored ones. These findings enhance our knowledge of archaeal community succession patterns in mangrove restoration, as well as provide fresh perspectives for the sustainable management of mangrove ecosystems.

Archaeal community composition as key driver of H2 consumption rates at the start-up of the biomethanation process

The performance of hydrogen consumption by various inocula derived from mesophilic anaerobic digestion plants was evaluated under ex situ biomethanation. A panel of 11 mesophilic inocula was operated at a concentration of 15 gVS.L−1 at a temperature of 35 °C in batch system with two successive injections of H2:CO2 (4:1 mol:mol). Hydrogen consumption and methane production rates were monitored from 44 h to 72 h. Hydrogen consumption kinetics varies significantly based on the inoculum origin, with no accumulation of volatile fatty acids. Microbial community analyses revealed that microbial indicators such as the increase in Methanosarcina sp. abundance and the increase of the Archaea/Bacteria ratio were associated to high initial hydrogen consumption rates. The improvement in the hydrogen consumption rate between the two injections was correlated with the enrichment in hydrogenotrophic methanogens. This work provides new insights into the early response of microbial communities to hydrogen injection and on the microbial structures that may favor their adaptation to the biomethanation process.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome.

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.

In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.

Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane.

Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.

Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures.

Forages and concentrates have consistently distinct patterns of fermentation in the rumen, with forages producing more methane (CH4) per unit of digested organic matter (OM) and higher acetate to propionate ratio than concentrates. A mechanism based on the Monod function of microbial growth has been proposed to explain the distinct fermentation pattern of forages and concentrates, where greater dilution rates and lower pH associated with concentrate feeding increase dihydrogen (H2) concentration through increasing methanogens growth rate and decreasing methanogens theoretically maximal growth rate, respectively. Increased H2 concentration would in turn inhibit H2 production, decreasing methanogenesis, inhibit H2-producing pathways such as acetate production via pyruvate oxidative decarboxylation, and stimulate H2-incorporating pathways such as propionate production. We examined the hypothesis that equalizing dilution rates in serial rumen cultures would result in a similar fermentation profile of a high forage and a high concentrate substrate. Under a 2 × 3 factorial arrangement, a high forage and a high concentrate substrate were incubated at dilution rates of 0.14, 0.28, or 0.56 h-1 in eight transfers of serial rumen cultures. Each treatment was replicated thrice, and the experiment repeated in two different months. The high concentrate substrate accumulated considerably more H2 and formate and produced less CH4 than the high forage substrate. Methanogens were nearly washed-out with high concentrate and increased their initial numbers with high forage. The effect of dilution rate was minor in comparison to the effect of the type of substrate. Accumulation of H2 and formate with high concentrate inhibited acetate and probably H2 and formate production, and stimulated butyrate, rather than propionate, as an electron sink alternative to CH4. All three dilution rates are considered high and selected for rapidly growing bacteria. The archaeal community composition varied widely and inconsistently. Lactate accumulated with both substrates, likely favored by microbial growth kinetics rather than by H2 accumulation thermodynamically stimulating electron disposal from NADH into pyruvate reduction. In this study, the type of substrate had a major effect on rumen fermentation largely independent of dilution rate and pH.

Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils

Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g−1 (dry soil) day−1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.

Composition of the rumen archaeal community of growing camels fed different concentrate levels.

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Natural peatlands represent a wide range of habitats that contribute to the conservation of biodiversity, including microbial biodiversity. Molecular biological methods make it possible to significantly increase the accounting of microbial diversity compared to the cultivation methods. The studies on microbial diversity in minerotrophic peatlands using molecular biological methods lag significantly behind such studies for ombrotrophic peatlands. In this work, we characterized the taxonomic composition and functional potential of the prokaryotic community of the minerotrophic pine swamp (fen) in the Tver region of northwestern Russia using high-throughput sequencing of 16S rRNA gene fragments. This study is unique, since it was carried out not in individual horizons but across the entire fen profile, taking into account the differentiation of the profile into the acrotelm and catotelm. The composition and dominants of bacterial and archaeal communities were determined not only at the level of phyla but also at the level of classes, families, and cultivated genera. The prokaryotic community of the studied fen was shown to have a high taxonomic diversity (28 bacterial and 10 archaeal phyla were identified). The profile differentiation of the taxonomic composition of prokaryotic communities is most clearly manifested in the analysis of the acrotelm and catotelm. In the bacterial communities of the acrotelm, the top three phyla included Acidobacteriota, Alphaproteobacteria, and Actinomycetota, in the catotelm—Betaproteobacteria, Bacteroidota, and Chloroflexota. In archaeal communities of the acrotelm, we discovered the monodominance of Nitrososphaerota, in the catotelm—the dominance of Bathyarchaeota and subdominance of Thermoplasmatota, Halobacterota, and Aenigmarchaeota. The hot spots of microbial diversity in the studied fen profile were found to be the 0–20 cm layer of the acrotelm and the 150–200 cm layer of the catotelm. In contrast to the taxonomic composition, the functional profiles of the prokaryotic communities of the acrotelm and catotelm were generally similar, except for methane metabolism, which was primarily carried out in the catotelm.

Effects of inocula on methane production and the microbial community in a rice straw anaerobic digestion system

Field experiments have shown that the mixed anaerobic digestion of straw with livestock and poultry manure can improve the efficiency of biogas production. We hypothesize that inoculation with livestock and poultry manure increase the efficiency of methane production by improving the diversity and structure of microbial community in the field anaerobic digestion system. In this study, an experimental system was established to simulate the microbial community of the mixed anaerobic digestion system in the field. The methane production and taxonomic composition of bacterial and archaeal communities in the rice straw anaerobic digestion systems were determined. We aim to reveal the effects of the inocula on the diversity and composition of bacterial and archaeal communities and the mechanism underlying the impact on biogas production in the field. The following results were obtained. (1) Inoculation significantly improved the efficiency of methane production in anaerobic digestion, and the best performance was achieved with treatment A (cleared biogas slurry), which obtained methane production that were 39.59 %, 106.85 %, and 123.00 % higher than in treatment B (pig manure extract), C (cleared biogas slurry + pig manure extract), and the control, respectively. (2) The inocula increased the abundance and diversity of bacterial communities in the early and middle stages and archaeal communities in the early stage. (3) The inocula also had a significant impact on bacterial and archaeal community composition in the early and middle stages. The inocula increased the relative abundance of Aquamicrobium_A, Proteiniphilum, and Cryptobacteroides but reduced the relative abundance of Macellibacteroides, Acinetobacter, and Phocaeicola. The dominant genus of archaeal community was altered from Methanosarcina to Methanocorpusculum. (4) It is concluded that inoculation significantly increase methane production as the inocula improve the abundance and diversity of bacteria and archaea of anaerobic digestion systems in the early and middle stages of digestion, as well as improve the structure and metabolic pathway of archaeal communities.

Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea

BackgroundDeclines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.ResultsOur findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.ConclusionsOur findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils.-4HQdD_EuWHa-cff1NJXs2Video

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BackgroundArchaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.ResultsThe relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.ConclusionsOur results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine.

Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.

Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge

The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.

Planktonic archaea reveal stronger dispersal limitation and more network connectivity than planktonic bacteria in the Jinsha River of southwestern China

Abstract Planktonic archaea and bacteria play important roles in biogeochemical cycling, but their biogeographical patterns and underlying ecological processes remain poorly understood, particularly in large‐scale rivers. We collected 43 water samples covering a 2279 km reach of the Jinsha River, one of the largest rivers in southwest China, and performed high‐throughput sequencing analysis on planktonic archaeal and bacterial communities. Partial Mantel analysis and neutral model were used to assess the factors influencing microbial distributions. The associations among different microbial species and their geographical distribution patterns were linked through co‐occurrence networks, and the putative key taxa in the archaeal and bacterial networks were analysed. The Shannon index of both archaeal and bacterial communities was highest in the midstream reach. The Pielou's evenness of archaea did not vary among the three reaches, whereas those of bacteria increased from upstream to downstream. The archaeal and bacterial community compositions were significantly different in the three reaches, but the differences among the bacterial communities were greater than among the archaeal communities. Both dispersal limitation and environmental selection affected the community compositions of the archaea and bacteria, but dispersal limitation was the most influential factor. Compared to archaea, bacteria were less affected by dispersal limitation and more by environmental selection. The co‐occurrence network analysis demonstrated that, compared with the bacterial network of all sites, the archaeal network with larger graph density had higher connectivity and complexity, but a lower proportion of negative correlations. The putative key taxa belonged to Nitrososphaeraceae and Candidatus_Nitrocosmicus from the archaeal community, and Hydrogenophaga and Sphingorhabdus from the bacterial community. Taken together, these findings demonstrated that the planktonic archaea were more dispersal‐limited and showed more network connectivity than the planktonic bacteria in the Jinsha River. This study enhances our understanding of the biogeographical distribution patterns and underlying ecological processes of planktonic microorganisms over large‐scale freshwater systems.

Robust cross-cohort gut microbiome associations with COVID-19 severity

ABSTRACT Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences. This alteration in gut microbiome configuration peaks at days 7–30 post diagnosis, after which the gut microbiome returns to a configuration that becomes more similar to that of healthy controls over time. Furthermore, we identified a core set of species that were consistently associated with disease severity across shotgun metagenomic and 16S cohorts, and whose abundance can accurately predict disease severity category of SARS-CoV-2 infected subjects, with Actinomyces oris abundance predicting population-level mortality rate of COVID-19. Additionally, we used relational diet-microbiome databases constructed from cohort studies to predict microbiota-targeted diet patterns that would modulate gut microbiota composition toward that of healthy controls. Finally, we demonstrated the association of disease severity with the composition of intestinal archaeal, fungal, viral, and parasitic communities. Collectively, this study has identified robust COVID-19 microbiome biomarkers, established accurate predictive models as a basis for clinical prognostic tests for disease severity, and proposed biomarker-targeted diets for managing COVID-19 infection.

Structure and Assembly Mechanism of Archaeal Communities in Deep Soil Contaminated by Chlorinated Hydrocarbons

Chlorinated hydrocarbons are typical organic pollutants in contaminated sites, and microbial remediation technology has attracted more and more attention. To study the structural characteristics and assembly mechanism of the archaeal community in chlorinated hydrocarbon-contaminated soil, unsaturated-zone soil within 2~10 m was collected. Based on high-throughput sequencing technology, the archaeal community was analyzed, and the main drivers, environmental influencing factors, and assembly mechanisms were revealed. The results showed that chlorinated hydrocarbon pollution altered archaeal community structure. The archaeal community composition was significantly correlated with trichloroethylene (r = 0.49, p = 0.001), chloroform (r = 0.60, p = 0.001), pH (r = 0.27, p = 0.036), sulfate (r = 0.21, p = 0.032), and total carbon (r = 0.23, p = 0.041). Under pollution stress, the relative abundance of Thermoplasmatota increased to 25.61%. Deterministic processes increased in the heavily polluted soil, resulting in reduced species richness, while positive collaboration among surviving species increased to 100%. These results provide new insights into the organization of archaeal communities in chlorinated hydrocarbon-contaminated sites and provide a basis for remediation activities.

Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia).

We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH4 metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities.