Archaeal Communities Research Articles

Sheaths are diverse and abundant cell surface layers in archaea.

Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell-cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.

Bacterial and Archaeal Communities within a High-altitude Soda Lake in the Qinghai-Tibet Plateau, China

Bacterial and Archaeal Communities within a High-altitude Soda Lake in the Qinghai-Tibet Plateau, China

Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China

Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km2. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.

Microbial community acclimation during anaerobic digestion of high-oil food waste

Anaerobic digestion is one of the most promising options for the disposal of biodegradable food waste. However, the relatively high content of oil in food waste inhibits the conversion efficiency of anaerobic digestion because of the accumulation of long-chain fatty acids (LCFAs). In this study, activated anaerobic sludge was acclimated to accommodate high-oil conditions. The methane yield of high-oil food waste digested by the acclimated sludge increased by 24.9% compared to that digested by the raw sludge. To determine the internal changes in the acclimated sludge, the shifts in the microbial communities during the acclimation period were investigated via high-throughput sequencing (HTS) based on the 16 S rRNA gene. The results indicated that Bacteroidetes, Firmicutes, Chloroflexi and Proteobacteria were the dominant bacteria at the phylum level. The acclimation time allows some functional bacterial taxa to proliferate, such as Clostridium and Longilinea, which are able to degrade LCFAs and turn them into small organic molecules that also have nutrient value for other bacteria. Among the archaeal communities, the hydrogenotrophic methanogen Methanobacterium nearly supplanted the acetotrophic methanogen Methanosaeta. The time profiles of volatile fatty acids (VFAs) and pH during this period provided additional evidence for the success of the acclimation. This study demonstrated the effectiveness of acclimation and the dynamic of microbial communities, which further contributed to the management and resource utilization of high-oil food waste.

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.

The microbiome of continuous wheat rotations: minor shifts in bacterial and archaeal communities but a source for functionally active plant-beneficial bacteria

Continuous wheat cropping often leads to yield decline, with suspected causes including increased pathogen susceptibility, decreased root growth, or low nutrient use efficiency, though the exact causes remain unknown. Here, we investigated soil and root-associated bacterial and archaeal communities in wheat under rotation versus continuous cultivation, monitored fungal pathogen presence, and used beneficial bacteria to mitigate Gaeumannomyces tritici (Ggt) symptoms in greenhouse experiments. Sampling was conducted at two field sites with different soil textures over two years and at two plant developmental stages, capturing site-specific and seasonal fluctuations. By cultivation, 767 bacterial isolates were screened for plant-beneficial traits. Amplicon sequencing revealed minor effects on community structure due to wheat rotational position but pronounced effects related to site, year, and microhabitat. Rhizoplane isolates with plant-beneficial traits were mainly Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Stenotrophomonas, and Variovorax. Continuous wheat rotations showed the highest proportion of bacteria with fungal antagonistic potential, indicating plant roots’ recruitment of beneficial bacteria. Introducing Ggt in the greenhouse experiment altered the bacterial and archaeal community, confirming field study results and demonstrating that applying beneficial bacteria early in the season at the seedling stage can control Ggt and improve plant growth. This study highlights the dynamic nature of wheat's below-ground bacterial and archaeal community, influenced by soil type, season, and microhabitat, with wheat rotation playing a minor role. In addition, it confirms the potential of selected Bacillus and Pseudomonas isolates, whether used individually or in consortia, for microbe-assisted mitigation of yield decline in intensive wheat production.

Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean.

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.

Potential functional profiling of soil microbial communities under long-term application of tannery sludge

This study investigated the impact of Cr contamination on the functional profiling of bacterial and archaeal communities in a tropical soil. The contaminated soil contained ∼300 mg kg⁻¹ of Cr due to the long-term application of tannery sludge. The FAPROTAX database was used to assess the potential functional profiling of bacterial and archaeal communities based on 16S rRNA gene phylogeny. The results showed a higher relative abundance of Actinobacteria, Proteobacteria, and Firmicutes. Additionally, an increased relative abundance of Bacillaceae and Paenibacillaceae was observed in Cr-contaminated soil. The functional profiling predicted eleven potential functions, with Cr contamination negatively affecting chemoheterotrophy, nitrification, ammonia oxidation, and nitrogen fixation. This study reveals that Cr contamination significantly impacts the functional profiling of soil bacterial and archaeal communities, emphasizing the importance of monitoring and mitigating Cr contamination to preserve soil function.

Metagenomic Analysis during Co-Digestion Buffalo Sludge and Tomato Pomace Post Thermal Stress: A Case Study

The tomato industry and buffalo farming generate waste, including sludge (BS) and tomato pomace (TP), which can significantly impact their economic and environmental sustainability. The case study tracked changes in microflora composition after a thermal shock during anaerobic co-digestion. The inoculum-to-substrate ratio was 0.5 based on volatile solid content under mesophilic conditions. An Automatic Methane Potential Test System was used to monitor the process before and after thermal stress (50°C) occurred for three days. Next-generation sequencing analyzed the bacterial and archaeal communities. The pH decreased, and methane production plateaued due to the high volatile solid content (87 g/L). After thermal stress, the pH returned to neutral, and the batch resumed biogas production. The cumulative CH4 production reached 3,115 Nml. The biogas had a maximum methane peak of 78.5% compared to 58.4% in BS. The taxonomic classification showed that Firmicutes (51.7%) and Bacteroidetes (29.9%) represented 81.6% of the total OTUs among the bacteria. Fonticella, the most abundant Clostridiaceae (average 4.3%), was absent in BS and increased (up to 17.1%) in TP during methane production. Methanocorpusculum was the most abundant in the archaeal community. However, Metanosarcina showed a stronger correlation with methane production. Brief thermal stress significantly altered bacterial and archaeal populations and allowed to resume biogas production.

Different macrophytes and eutrophic gradients regulate microbial communities of phytoremediation for eutrophication pollution and carbon reduction

Phytoremediation on eutrophicated ecosystems has received growing research interest, and macrophytes and eutrophic gradients are considered as key influencing factors. This study used Vallisneria natans, Iris pseudacorus, and their mixed plantings in aquatic ecosystems (9 m × 2 m × 0.5 m, L × W × D) receiving increased eutrophic nitrogen and phosphorus gradients (4, 40, 80 mg/L of nitrogen and 0.4, 4, 8 mg/L of phosphorus), to unveil phytoremediation effects and corresponding microbial mechanisms. Different phytoremediations could effectively improve water quality with removal efficiencies of 57.4%–98.7% on ammonium, 45.7%–93.7% on total nitrogen, 46.7%–100% on available phosphorus, and 38.4%–95.2% on total phosphorus, respectively. Macrophytes and eutrophic gradients jointly affected diversities, compositions, structures, interactions, and functions of sedimental bacterial and archaeal communities. Microbial diversities increased with macrophytes presence and increased eutrophic gradients. Principal component analysis demonstrated that different macrophytes diverged microbial community structures, and increment of eutrophic gradients reduced structural dissimilarities. Dominant compositional communities, including Chloroflexi, Firmicutes, Proteobacteria, Anaerolineae, and Nitrososphaeria, were also keystone taxa of community co-occurrence networks in phytoremediations. Increased eutrophic gradients enhanced microbial cooperative interactions, whilst V. natans fostered bacterial interactions, and I. pseudacorus and mixed plantings strengthened archaeal interactions. Functional prediction indicated that bacterial “phosphate transferase” and archaeal “methanogenesis” were significantly reduced, whilst archaeal “nitrification”, “denitrification”, “comammox”, and “methane oxidation” were elevated by macrophytes and eutrophic gradients, indicating likely mechanisms for nutrient and GHGs metabolisms. This study extended our knowledge on microbial mechanisms of phytoremediations with different macrophytes treating eutrophicated waters of increased gradients, therefore providing references for further developing phytoremediation technologies.

Regulating Leaf Photosynthesis and Soil Microorganisms through Controlled-Release Nitrogen Fertilizer Can Effectively Alleviate the Stress of Elevated Ambient Ozone on Winter Wheat.

The mitigation mechanisms of a kind of controlled-release nitrogen fertilizer (sulfur-coated controlled-release nitrogen fertilizer, SCNF) in response to O3 stress on a winter wheat (Triticum aestivum L.) variety (Nongmai-88) were studied in crop physiology and soil biology through the ozone-free-air controlled enrichment (O3-FACE) simulation platform and soil microbial metagenomics. The results showed that SCNF could not delay the O3-induced leaf senescence of winter wheat but could enhance the leaf size and photosynthetic function of flag leaves, increase the accumulation of nutrient elements, and lay the foundation for yield by regulating the release rate of nitrogen (N). By regulating the soil environment, SCNF could maintain the diversity and stability of soil bacterial and archaeal communities, but there was no obvious interaction with the soil fungal community. By alleviating the inhibition effects of O3 on N-cycling-related genes (ko00910) of soil microorganisms, SCNF improved the activities of related enzymes and might have great potential in improving soil N retention. The results demonstrated the ability of SCNF to improve leaf photosynthetic function and increase crop yield under O3-polluted conditions in the farmland ecosystem, which may become an effective nitrogen fertilizer management measure to cope with the elevated ambient O3 and achieve sustainable production.

Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.

Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication.

The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

Evolution mechanism of microbial community structure and metabolic activity in aquatic nutrient-poor sedimentary environments driven by 17β-estradiol pollution.

17β-Estradiol (E2) is a novel micro-pollutant that is widely distributed in aquatic sediments and has a universal toxicological effect on aquatic organisms. However, its ecological impact on aquatic microorganisms is not yet clear. In this study, we designed a simulation system for oligotrophic water deposition in the laboratory, analyzed the impact of different concentrations of E2 pollution on the carbon metabolism activity (carbon gas emission rate) of water microorganisms. Based on high-throughput sequencing results, we revealed the impact of E2 pollution on the community structure succession and metabolic function of bacteria, archaea, and methanogens in the simulated system, explored the impact mechanism of E2 pollution on microbial carbon metabolism in water bodies. Our results suggested that E2 significantly impacts the bacterial and archaeal community rather than the methanogen community, thereby indirectly inhibiting methane production. The achievements will bridge the theoretical gap between estrogen metabolism and carbon metabolism in sedimentary environments and contribute to enriching the ecological toxicology theory of steroid estrogen.

Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.

Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.

Microbial DNA sample preservation and possible artifacts for field-based research in remote tropical peatlands

Surveying bacterial and archaeal microbial communities in host and environmental studies requires the collection and storage of samples. Many studies are conducted in distant locations challenging these prerequisites. The use of preserving buffers is an important alternative when lacking access to cryopreservation, however, its effectivity for samples with challenging chemistry or samples that provide opportunities for fast bacterial or archaeal growth upon exposure to an aerobic environment, like peat samples, requires methodological assessment. Here, in combination with an identified optimal DNA extraction kit for peat soil samples, we test the application of several commercial and a homemade preservation buffer and make recommendations on the method that can most effectively preserve a microbiome reflective of the original state. In treatments with a non-optimal buffer or in the absence, we observed notable community shifts beginning as early as three days post-preservation lowering diversity and community evenness, with growth-driven artifacts from a few specific phyla. However other buffers retain a very close composition relative to the original state, and we described several metrics to understand some variation across them. Due to the chemical effects of preservation buffers, it is critical to test their compatibility and reliability to preserve the original bacterial and archaeal community in different environments.

Vadose-zone characteristic pollutants distribution, microbial community structure and functionality changes in response to long-term leachate pollution of an informal landfill site

The study embarked on a comprehensive examination of the evolution and diversity of microorganisms within long-term leachate pollution environments, with a focus on varying depths and levels of contamination, and its linkage to soil characteristics and the presence of heavy metals. It was observed that microbial diversity presented distinct cross-depth trend, where archaeal communities were found to be particularly sensitive to alterations in soil depth. Noteworthily, Euryarchaeota increased by 4.82 %, 7.64 % and 9.87 % compared with topsoil. The abundance of Tahumarchaeota was successively reduced by 5.79 %, 9.58 %, and 12.66 %. The bacterial community became more sensitive to leachate pollution, and the abundance of Protebacteria in contaminated soil decreased by 10.27 %, while the abundance of Firmicutes increased by 7.46 %. The bacterial genus Gemmobacter, Chitinophaga and Rheinheimera; the archaeal genus Methanomassiliicoccus and Nitrosopumilus; along with the fungal genus Goffeauzyma, Gibberella, and Setophaeosphaeria emerged as pivotal biological markers for their respective domains, underpinning the biogeochemical dynamics of these environments. Furthermore, the study highlighted that geochemical factors, specifically nitrate (NO₃−-N) levels and humic acid (HA) fractions, played crucial roles in modulating the composition and metabolic potential of these communities. Predictive analyses of functional potentials suggested that the N functional change of archaea was more pronounced, with anaerobic ammonia oxidation and nitrification decreased by 15.78 % and 14.62 %, respectively. Overall, soil characteristics alone explained 57.9 % of the total variation in the bacterial community structure. For fungal communities within contaminated soil, HMs were the primary contributors, explaining 46.9 % of the variability, while soil depth accounting for 6.4 % of the archaeal variation. This research enriches the understanding of the complex interrelations between heavy metal pollution, soil attributes, and microbial communities, paving the way for informed strategies in managing informal landfill sites effectively.

Soil Microbial Community Structure and Its Contribution to Carbon Cycling in the Yalu River Estuary Wetland

Wetland microbial communities play a vital role in ecosystem functioning, particularly in the intricate processes of carbon cycling. This study employed metagenomic sequencing to investigate the diversity, composition, structural differences, carbon cycling functional gene, and microbial species of soil microbial communities in five distinct soil types of the Yalu River estuary wetland, including shoal soil, bog soil, paddy soil, meadow soil, and brown forest soil. We further explored the influence of environmental factors on both the microbial community structure and carbon cycling functional genes. Our results revealed a bacterial-dominated soil microbial community, constituting about 97.6%. Archaea and fungi represented relatively minor fractions, at 1.9% and 0.4%, respectively. While no significant differences were observed in Chao1 indices between bacterial and fungal communities, the Shannon index revealed notable differences. Both Chao1 and Shannon indices exhibited significant variations within the archaeal communities. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae. Thaumarchaeota, Crenarchaeota, and Euryarchaeota formed the major archaeal phyla, while Ascomycota, Mucoromycota, and Basidiomycota were the dominant fungal phyla. Non-metric multidimensional scaling (NMDS) analysis based on Bray-Curtis distance revealed notable differences in the bacterial, archaeal, and fungal community structures across the samples. Redundancy analysis (RDA) identified key environmental factors for the major phyla. Soil pH, soil organic carbon (SOC), electrical conductivity (EC), and total phosphorus (TP) were the main influencing factors for bacteria, while soil TP, EC, total sulfur (TS), and SOC were the primary drivers for archaeal phyla. Soil total nitrogen (TN) and EC were the main influencing factors for fungal phyla. Analysis of key carbon cycling pathway genes utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and clustering heatmap revealed some variations in functional gene composition across different soil types. Mantel test indicated that pH, TN, and SOC were the primary environmental factors influencing microbial functional genes associated with soil carbon cycling. Stratified bar chart analysis further demonstrated that the major contributors to carbon cycling originated from corresponding dominatnt phyla and genera of Proteobacteria, Thaumarchaeota, Actinomycetota, Euryarchaeota, and Bacteroidota. The species and relative abundance of microorganisms associated with carbon cycling pathways varied among the samples. These findings provide a crucial reference for informing the conservation and sustainable management of wetland ecosystems in the Yalu River estuary.

Responses of soil microbial diversity, network complexity and multifunctionality to environments changes in volcanic ecosystems

Volcanic ecosystems with unique and reduced-complexity environments are distributed globally, providing a platform for analysing the structure and function of natural microbial communities. This study aimed to explore the responses of soil microbial diversity, network complexity, and multifunctionality to environments changes in volcanic ecosystems. Actinobacteria (26.00–46.26 %), Acidobacteriota (5.68–19.10 %), and Crenarchaeota (4.71–18.65 %) were the dominant prokaryotic phyla. Furthermore, bacterial community was dominant over archaeal community. Among the fungal phyla, Ascomycota accounted for 60.30–94.45 % of the relative abundance. Fungal communities were more sensitive to the changes in biogeographical patterns in volcanic soils, while the prokaryotic community was more diverse. There were more biomarkers and functional compositions at the bottom of volcano sites than at the top (biomarkers: 85 vs. 39; functional group: 18 vs. 2; ecological guild: 8:1). The networks at the bottom of volcano had an increased complexity and connectivity (higher avgK and avgCC; shorter GD). The network in the top volcano was highly modularised. Three keystone species were observed only in this network. Soil chemical factors, directly and indirectly, influenced microbial structure and multifunctionality. Therefore, this study may provide key insights into understanding the assemblage of soil microbial communities in extreme environments, such as volcanic areas.

Enhancement of Biodegradability of Chicken Manure via the Addition of Zeolite in a Two-Stage Dry Anaerobic Digestion Configuration.

Leach bed reactors (LBRs) are dry anaerobic systems that can handle feedstocks with high solid content, like chicken manure, with minimal water addition. In this study, the chicken manure was mixed with zeolite, a novel addition, and packed in the LBR to improve biogas production. The resulting leachate was then processed in a continuous stirred tank reactor (CSTR), where most of the methane was produced. The supernatant of the CSTR was returned to the LBR. The batch mode operation of the LBR led to a varying methane production rate (MPR) with a peak in the beginning of each batch cycle when the leachate was rich in organic matter. Comparing the MPR in both systems, the peaks in the zeolite system were higher and more acute than in the control system, which was under stress, as indicated by the acetate accumulation at 2328 mg L-1. Moreover, the presence of zeolite in the LBR played a crucial role, increasing the overall methane yield from 0.142 (control experiment) to 0.171 NL CH4 per g of volatile solids of chicken manure entering the system at a solid retention time of 14 d. Zeolite also improved the stability of the system. The ammonia concentration increased gradually due to the little water entering the system and reached 3220 mg L-1 (control system) and 2730 mg L-1 (zeolite system) at the end of the experiment. It seems that zeolite favored the accumulation of the ammonia at a lower rate (14.0 mg L-1 d-1) compared to the control experiment (17.3 mg L-1 d-1). The microbial analysis of the CSTR fed on the leachate from the LBR amended with zeolite showed a higher relative abundance of Methanosaeta (83.6%) compared to the control experiment (69.1%). Both CSTRs established significantly different bacterial profiles from the inoculum after 120 days of operation (p < 0.05). Regarding the archaeal communities, there were no significant statistical differences between the CSTRs and the inoculum (p > 0.05).