Microbial Community Shifts Research Articles

Response of soil microbial community structure to temperature and nitrogen fertilizer in three different provenances of Pennisetum alopecuroides.

Soil microorganisms are key indicators of soil health, and it is crucial to investigate the structure and interactions of soil microbial communities among three different provenances of Pennisetum alopecuroides under varying nitrogen fertilizer and temperature levels in Northwest China. This study aims to provide theoretical support for the sustainable use of artificial grassland in this region. Employing a two-factor pot-control experiment with three nitrogen fertilizer treatments and three temperature treatments, a total of all treatments was utilized to examine the composition and abundance of soil microbial communities associated with Pennisetum alopecuroides using high-throughput sequencing, PCR technology, and molecular ecological network analysis. The results revealed that Proteobacteria was the dominant bacterial phylum while Ascomycota was the dominant fungal phylum in the soil samples from three provenances of Pennisetum. Specifically, Proteobacteria exhibited higher abundance in the N3T2 treatment compared to other treatments under N3T2 (25-30°C, 3 g/pot) treatment conditions in Shaanxi and Gansu provinces; similarly, Proteobacteria was more abundant in the N1T2 (25-30°C, 1 g/pot) treatment in Inner Mongolia under N1T2. Moreover, Ascomycota displayed higher abundance than other treatments in both Inner Mongolia and Gansu provinces. Additionally, Pennisetum Ascomycota demonstrated greater prevalence under (25-30°C, 3 g/pot) treatment compared to other treatments; furthermore, Shaanxi's Pennisetum Ascomycota exhibited increased prevalence under N3T1 (18-23°C, 3 g/pot) treatment compared to other treatments. The richness and diversity of soil microbial communities were significantly influenced by nitrogen fertilizer and temperature changes, leading to notable alterations in their structure. Molecular ecological network analyses revealed strong collaborative relationships among microbial species in Shaanxi Pennisetum and Inner Mongolia Pennisetum under high nitrogen and high temperature treatments, while competitive relationships were observed among microbial species in Gansu Pennisetum under similar conditions. Redundancy analysis indicated that soil pH, total potassium, and total phosphorus were the primary environmental factors influencing microorganisms. In summary, this study offers a theoretical foundation for assessing the sustainable utilization of Pennisetum artificial grasslands in Northwest China by investigating the shifts in soil microbial communities and the driving factors under varying nitrogen fertilizer and temperature levels.

Using a combination of phospholipid fatty acids profiles and DNA-based sequencing analyses to detect shifts in the biofloc microbial community in different carbon sources and carbon/nitrogen ratios.

A 35-day study investigated the impact of carbon sources and carbon/nitrogen (C/N) ratios on the microbial community of biofloc. For this purpose, we utilized a combination of phospho-lipid fatty acids (PLFAs) profiles and DNA-based sequencing methods to investigate changes in the microbial community composition and structure. The experiment involved three carbon sources including Dextrin (DEX), corn starch (CS) and wheat bran (WB) at two C/N ratios (19 and 30). The results indicated that WB and CS were found to decrease nitrogen metabolite concentration while increasing total suspended solids and bacterial density compared to DEX. The treatments exhibited variations in microbial communities and the use of polymerase chain reaction/ denaturing gradient gel electrophoresis analysis revealed distinct dominant bacterial species linked to carbon sources and C/N ratios. Furthermore, the highest levels of bacteria and protozoa PLFAs biomarkers were observed in the C/N30 ratio and WB treatment while the ratio for poly-β-hydroxybutyrate/PLFAs and fungi biomarkers displayed a decrease. Also, by incorporating the results of PLFAs profile and conducting a principal component analysis, the treatments were categorized into distinct groups based on both the carbon source and C/N ratios. Overall, both methods yield consistent results. PLFAs offered additional insights into the microbial composition beyond bacterial structure while DNA-based analysis provided finer taxonomic resolution.

Biomass attachment and microbiota shifts during porcine faecal in vitro fermentation of almond and macadamia nuts differing in particle sizes.

Nuts are highly nutritious and good sources of dietary fibre, when consumed as part of a healthy human diet. Upon consumption, nut particles of various sizes containing lipids entrapped by the plant cell walls enter the large intestine where they are fermented by the resident microbiota. This study investigated the microbial community shifts during in vitro fermentation of almond and macadamia substrates, of two particle sizes including fine particles (F = 250-500 μm) and cell clusters (CC = 710-1000 μm). The aim was to determine how particle size and biomass attachment altered the microbiota. Over the 48 h fermentation duration, short chain fatty acid concentrations increased due to particle size rather than nut type (almond or macadamia). However, nut type did change microbial population dynamics by stimulating specific genera. Tyzzerella, p253418B5 gut group, Lachnospiraceae UCG001, Geotrichum, Enterococcus, Amnipila and Acetitomaculum genera were unique for almonds. For macadamia, three unique genera including Prevotellaceae UCG004, Candidatus Methanomethylophilus and Alistipes were noted. Distinct shifts in the attached microbial biomass were noted due to nut particle size. Bacterial attachment to nut particles was visualised in situ during fermentation, revealing a decrease in lipids and an increase in attached bacteria over time. This interaction may be a pre-requisite for lipid breakdown during nut particle disappearance. Overall, this study provides insights into how nut fermentation alters the gut microbiota and the possible role that gut microbes have in lipid degradation.

Seasonal Change of Sediment Microbial Communities and Methane Emission in Young and Old Mangrove Forests in Xuan Thuy National Park.

Microbial communities in mangrove forests have recently been intensively investigated to explain the ecosystem function of mangroves. In this study, the soil microbial communities under young (<11 years-old) and old (>17 years-old) mangroves have been studied during dry and wet seasons. In addition, biogeochemical properties of sediments and methane emission from the two different mangrove ages were measured. The results showed that young and old mangrove soil microbial communities were significantly different on both seasons. Seasons seem to affect microbial communities more than the mangrove age does. Proteobacteria and Chloroflexi were two top abundant phyla showing >15%. Physio-chemical properties of sediment samples showed no significant difference between mangrove ages, seasons, nor depth levels, except for TOC showing significant difference between the two seasons. The methane emission rates from the mangroves varied depending on seasons and ages of the mangrove. However, this did not show significant correlation with the microbial community shifts, suggesting that abundance of methanogens was not the driving factor for mangrove soil microbial communities.

Responses of bacterial communities and nitrogen-cycling microbiomes to the conversion from cereals to legumes in the rice-based system

Legumes are gaining popularity in rice-centric agroecosystems to boost yield, improve sustainability, and enhance soil fertility. However, their effects on soil nitrogen(N)-transforming networks, and predominant drivers governing microbial communities shift remain largely opaque. Here, we investigated soil bacterial community composition and N-cycling genes after converting to legume rotations in a 7-year field experiment for both rice and winter cropping seasons. Two conventional rice-based systems, rice-wheat (RW) and rice-rape (RRa), and four rice-legume rotations, rice-milk vetch (RM), rice-fava bean (RF), rice-milk vetch-rice-fava bean after continuous rice-milk vetch (RMF), and rice-fava bean-rice-milk vetch following continuous rice-fava bean (RFM) were constructed. Results showed that legume integration imposed greater impacts on soil biogeochemistry properties and bacterial communities in winter versus rice seasons. Integration of legume into rice-based cropping systems elicited significant alterations in soil water content, CEC, pH, total N content (TN), microbial biomass N, and dissolved organic carbon. Taxa including Acidobacteria (RFM), Rokubacteria (RMF), and Chloroflexi (RM) related to decomposition potentials were altered. Shift in soil bacterial community were attributed to alterations in environmental factors including soil pH, CEC, and TN. Legume mulching during rice seasons significantly reduced potential for assimilatory nitrite reduction (RM). Legume cultivation, on the other hand, suppressed the processes of N fixation (RFM), nitrate and nitrite reduction (RF and RFM) during winter seasons, potentially decreasing N leaching and N2O emissions. This study demonstrates strategic legume integration can reshape soil N cycling to improve agricultural sustainability.

Responses of grape yield and quality, soil physicochemical and microbial properties to different planting years

As an economically important fruit crop, continuous cropping of grapes can potentially impact soil health resulting in decreased yields. However, the mechanism of how soil microecological environment affects grape quality at different growth stages is not fully understood. A field experiment was conducted to investigate the effects of continuous grape cultivation for 0, 7, and 12 (CK, G7Y and G12Y) years on soil physicochemical properties and microbial community at different growth periods and soil depths, as well as on grape yield and quality. The results showed that grape yield, aroma compound contents, soil and grape leaf nutrients decreased significantly with the increase of planting years, soil acidification and secondary salinization intensified. Compared to G7Y, the relative abundance of the beneficial soil microorganisms Mortierella, Bacillus and Pseudomonas decreased significantly in G12Y, while the relative abundance of the potential pathogenic fungi Pseudaleuria and Aspergillus increased significantly. In addition, the nutrient content and biomarkers in the subsoil were lower than those in the topsoil. Particularly, the fruit setting stage appeared to be more sensitive to shifts in soil microbial communities over different planting years. Correlation analysis showed that grape yield was positively correlated with Bacillus and Mortierella, and negatively correlated with Fusarium. Grape yield was more sensitive to phosphorus and potassium fertilizers than to nitrogen fertilizer. In conclusion, continuous cropping reduced the content of soil nutrients and the number of soil beneficial microorganisms, increased the abundance of soil pathogenic microorganisms, and jointly caused changes in grape yield and quality. Therefore, it is necessary to optimize the management strategies to improve the soil microbial diversities especially beneficial microbial diversity to maintain the soil health and then to promote sustainable production of vineyards.

Impact of waste separation on the biological nitrogen removal in a MSW incineration leachate treatment plant: Performance and microbial community shift

After waste separation program was launched in China in 2019, incineration leachate treatment plants are facing a challenge of effective removal of nitrogen from leachate due to lack of sufficient carbon source. In this study, the performance of a biological incineration leachate treatment process (anaerobic digestion (AD) - two-stage anoxic/aerobic (A/O) process) was evaluated after adopting the waste separation program, and the changes in the microbial community and function was analyzed using 16S rRNA amplicon sequencing technology. Results showed that after the waste separation, the influent chemical oxygen demand (COD) concentration reduced by 90% (from 19,300 to 1780 mg L−1) with the COD/N ratio decreased from 12.3 to 1.4, which led to a decreased nitrogen removal efficiency (NRE) of <65% and a high effluent NO3− accumulation (445.8–986.5 mg N·L−1). By bypassing approximately 60% of the influent to the two-stage A/O process and adding external carbon source (glucose), the mean NRE increased to 86.3 ± 7.4%. Spearman's analysis revealed that refractory compounds in the bypassed leachate were closely related to the variations in bacterial community composition and nitrogen removal function in the two-stage A/O, leading to a weakened correlation of microbial network. KEGG functional pathway predictions based on Tax4Fun also confirmed that the bypassed leachate induced xenobiotic compounds to the two-stage A/O process, the relative abundance of nitrogen metabolism was reduced by 32%, and more external carbon source was required to ensure the satisfactory nitrogen removal of >80%. The findings provide a good guide for regulation of incineration leachate treatment processes after the waste separation.

Drought Shifts Sorghum Root Metabolite and Microbiome Profiles and Enriches for Pipecolic Acid

Plant-associated microbial communities shift in composition as a result of environmental perturbations, such as drought. It has been shown that Actinobacteria are enriched in plant roots and rhizospheres during drought stress. However, the correlations between microbiome dynamics and plant response to drought are poorly understood. Here we apply a combination of bacterial community composition analysis and plant metabolite profiling in Sorghum bicolor roots, rhizospheres, and soil during drought and drought recovery to investigate potential contributions of host metabolism to shifts in bacterial composition. Our results provide a detailed view of metabolic shifts across the plant root during drought and show that the response to rewatering differs between root and soil; additionally, we identify drought-responsive metabolites that are highly correlated with the observed changes in Actinobacteria abundance. Furthermore, we find that pipecolic acid is a drought-enriched metabolite in sorghum roots, and that exogenous application of pipecolic acid inhibits root growth. Finally, we show that this activity functions independent of the systemic acquired resistance pathway and has the potential to impact Actinobacterial taxa within the root microbiome.

A dynamics association study of gut barrier and microbiota in hyperuricemia.

The intricate interplay between gut microbiota and hyperuricemia remains a subject of growing interest. However, existing studies only provided snapshots of the gut microbiome at single time points, the temporal dynamics of gut microbiota alterations during hyperuricemia progression and the intricate interplay between the gut barrier and microbiota remain underexplored. Our investigation revealed compelling insights into the dynamic changes in both gut microbiota and intestinal barrier function throughout the course of hyperuricemia. The hyperuricemia mice (HY) were given intragastric administration of adenine and potassium oxalate. Gut microbiota was analyzed by 16S rRNA sequencing at 3, 7, 14, and 21 days after the start of the modeling process. Intestinal permeability as well as LPS, TNF-α, and IL-1β levels were measured at 3, 7, 14, and 21 days. We discovered that shifts in microbial community composition occur prior to the onset of hyperuricemia, key bacterial Bacteroidaceae, Bacteroides, and Blautia exhibited reduced levels, potentially fueling microbial dysbiosis as the disease progresses. During the course of hyperuricemia, the dynamic fluctuations in both uric acid levels and intestinal barrier function was accompanied with the depletion of key beneficial bacteria, including Prevotellaceae, Muribaculum, Parabacteroides, Akkermansia, and Bacteroides, and coincided with an increase in pathogenic bacteria such as Oscillibacter and Ruminiclostridium. This microbial community shift likely contributed to elevated lipopolysaccharide (LPS) and pro-inflammatory cytokine levels, ultimately promoting metabolic inflammation. The decline of Burkholderiaceae and Parasutterella was inversely related to uric acid levels, Conversely, key families Ruminococcaceae, Family_XIII, genera Anaeroplasma exhibited positive correlations with uric acid levels. Akkermansiaceae and Bacteroidaceae demonstrating negative correlations, while LPS-containing microbiota such as Desulfovibrio and Enterorhabdus exhibited positive correlations with intestinal permeability. In summary, this study offers a dynamic perspective on the complex interplay between gut microbiota, uric acid levels, and intestinal barrier function during hyperuricemia progression. Our study suggested that Ruminiclostridium, Bacteroides, Akkermansiaceae, Bilophila, Burkholderiaceae and Parasutterella were the key bacteria that play vital rols in the progress of hyperuricemia and compromised intestinal barrier, which provide a potential avenue for therapeutic interventions in hyperuricemia.

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

Establishment of plastic-associated microbial community from superworm gut microbiome

Gut microbial communities of plastic-munching worms provide novel insights for the development of plastic-processing biotechnologies. Considering the complexity of worm maintenance and the gut microbial communities, it is challenging to apply the worms directly in plastic processing. Harnessing the power of microbial communities derived from the worm gut microbiomes in vitro may enable a promising bioprocess for plastic degradation. Here, we established stable and reproducible plastic-associated biofilm communities derived from the gut microbiome of a superworm, Zophobas atratus, through a two-stage enrichment process: feeding with plastics (HDPE, PP, and PS) and in vitro incubation of gut microbiomes obtained from the plastic-fed worms. Plastic feeding exhibited marginal influence on bacterial diversity but substantially changed the relative abundance of different bacterial groups, and intriguingly, enriched potential plastic degraders. More prominent shifts of microbial communities were observed during the in vitro incubation of the gut microbiomes. Taxa containing plastic-degrading strains were further enriched, while other taxa represented by lactic acid bacteria were depleted. Additionally, the plastic characterization confirmed the degradation of the incubated plastics by the plastic-associated microbial communities. Community functional inference for both gene abundance and community phenotype suggested that the in vitro incubation enhanced plastic-degrading potential. Deterministic ecological effects, in particular, selection processes, were identified as the main driving force of the observed community shifts. Our findings provide novel insights into plastic-munching-worm-inspired bioprocessing of plastic wastes.

Shift in the rhizosphere microbial communities between growing- and low-temperature dormant seasons in a northern hardwood forest

Shift in the rhizosphere microbial communities between growing- and low-temperature dormant seasons in a northern hardwood forest

Drought-induced tree mortality in Scots pine mesocosms promotes changes in soil microbial communities and trophic groups

Increased tree mortality related to water limitation is documented for various species at different sites globally. Nevertheless, our understanding of tree mortality effects on soil microbial communities remains scarce. Therefore, we conducted a mesocosm experiment with young Scots pine saplings and natural forest soil with differing drought legacies to follow changes in soil microbial communities during tree mortality. Scots pine saplings were completely deprived of water during the experiment until they died. Shifts in soil microbial communities during tree mortality were assessed by metabarcoding in parallel with measurements of tree vitality and physicochemical soil properties. Drought history influenced the rate at which trees died, although high individual differences were observed. Tree death was accompanied by reduced stomatal conductance, discoloring of needles, increased defoliation, and shrinkage of the stem diameter. Soil NO3− concentrations increased after tree death, potentially through diminished plant uptake and increased microbial nitrification. Microbial abundance and community composition were affected by tree death and drought legacy. Copiotrophic bacterial taxa decreased during tree mortality, while oligotrophic taxa increased, probably slowing down soil carbon turnover. Fungal saprotrophs decreased, while symbiotrophs, such as ectomycorrhizal (ECM) fungi, increased in abundance, potentially through facultative saprothrophy and as a survival strategy of the trees in the initial phase of dying. Overall, our results indicate that drought-induced tree mortality promotes changes in soil prokaryotic and fungal communities, potentially affecting soil processes in forest ecosystems.

The Salinity Survival Strategy of Chenopodium quinoa: Investigating Microbial Community Shifts and Nitrogen Cycling in Saline Soils.

Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa's salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg-1, 3 g·kg-1, and 6 g·kg-1) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. Choroflexi, Acidobacteriota, and Myxococcota were inhibited by increased salinity, while the relative abundance of Bacteroidota increased. Proteobacteria and Actinobacteria showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (nirS, nosZ), upregulating nitrification genes (Archaeal amoA (AOA), Bacterial amoA (AOB)), and stabilizing nitrogen fixation genes (nifH) to absorb nitrate-nitrogen (NO3-_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments.

New perspectives on microbiome and nutrient sequestration in soil aggregates during long‐term grazing exclusion

AbstractGrazing exclusion alters grassland soil aggregation, microbiome composition, and biogeochemical processes. However, the long‐term effects of grazing exclusion on the microbial communities and nutrient dynamics within soil aggregates remain unclear. We conducted a 36‐year exclusion experiment to investigate how grazing exclusion affects the soil microbial community and the associated soil functions within soil aggregates in a semiarid grassland. Long‐term (36 years) grazing exclusion induced a shift in microbial communities, especially in the &lt;2 mm aggregates, from high to low diversity compared to the grazing control. The reduced microbial diversity was accompanied by instability of fungal communities, extended distribution of fungal pathogens to &gt;2 mm aggregates, and reduced carbon (C) sequestration potential thus revealing a negative impact of long‐term GE. In contrast, 11–26 years of grazing exclusion greatly increased C sequestration and promoted nutrient cycling in soil aggregates and associated microbial functional genes. Moreover, the environmental characteristics of microhabitats (e.g., soil pH) altered the soil microbiome and strongly contributed to C sequestration. Our findings reveal new evidence from soil microbiology for optimizing grazing exclusion duration to maintain multiple belowground ecosystem functions, providing promising suggestions for climate‐smart and resource‐efficient grasslands.

PSI-8 Effect of Monensin Withdrawal on the Rumen Prokaryote Microbiome in Bos Indicus and Bos Taurus Steers Consuming Bermudagrass Hay

Abstract Monensin, a carboxylic polyether ionophore, is commonly added to ruminant diets as a strategy for improving animal production by altering ruminal fermentation. However, research concerning the effect of monensin withdrawal is limited. Therefore, the effect of monensin withdrawal and the subspecies of cattle on the rumen prokaryote microbiome was evaluated using ruminally cannulated steers (5 Bos indicus, BI and 5 Bos taurus, BT; 398 kg BW) consuming bermudagrass hay (13.7% CP). Subspecies were concurrently subjected to a two period, two treatment crossover design. Each 70-d period consisted of a 42 d adaptation phase with treatments including 0 (CON) or 200 (MON) mg·animal-1 monensin (Rumensin 90; Elanco Animal Health, Greenfield, IN) fed in 0.91 kg dried distillers grains with solubles daily. Withdrawal of monensin was then evaluated for a 28-d phase following adaptation. Rumen fluid was collected via suction strainer from the dorsal and ventral sacs of the rumen at feeding on d 1, 7, 14, 21, and 28 of the withdrawal phase and frozen until further analysis. Upon completion of the trial, samples were thawed and analyzed for microbial populations using massively parallel sequencing. The V4 region of the 16S rRNA gene was sequenced to analyze and compare rumen prokaryotic microbes within treatment groups and subspecies. Sequences were processed using QIIME 2 (q2) version 2021.2 and imported into R v4.1 for statistical analysis and graphical displays. Bray Curtis-based principle coordinate analysis (PCoA) provided visualization of microbial community clustering by monensin treatment and subspecies, facilitating identification of microbial community shifts resulting from treatments or subspecies. No monensin×subspecies×day interaction (P = 0.96) was observed. However, an effect of monensin (P = 0.01), subspecies (P ≤ 0.01), and day (P = 0.017) on the microbiome was present. The changes in microbial density that were observed with monensin withdrawal help to provide insight into the mode of action of monensin and its impact on potential methane mitigation in cattle.

Nanoparticle-assisted biohydrogen production from pretreated food industry wastewater sludge: Microbial community shifts in batch and continuous processes

Biohydrogen production from industrial waste has gained a significant attention as a sustainable energy source. In this study, the enrichment of biohydrogen production from pretreated dissolved air flotation (DAF) sludge, generated from food industry wastewater treatment plants, was investigated using SiO2@Cu-Ag dendrites core–shell nanostructure (NS). The effect of NS on the changes of the microbial community and biohydrogen yield was evaluated through batch and continuous tests. In batch mode, various nanomaterial doses were investigated with several concentrations ranging from 20 to 50 mg/L for hydrogen production using glucose as a substrate. The optimum core–shell NS amount was 40 mg/L, achieving a maximum H2 yield of 163 mL/g volatile solids (VS) compared to the control's 79 mL/g VS. However, 50 mg/L NS inhibited most bacteria in the sludge. The continuous experiment used a continuous stirring tank reactor (CSTR) with 40 mg/L SiO2@Cu-Ag core–shell NS and pretreated industrial sludge as substrate. The H2 yield increased to 115 L/kg VS compared to the control reactor's 89 L/kg VS. The gas analysis showed compositional proportions of 83 % H2, 7 % CO2, and 4.5 % methane, while the microbial community analysis indicated the development of hydrogen-producing species such as Clostridium. In conclusion, SiO2@Cu-Ag core–shell NS addition enhanced anaerobic degradation of organic matter and its conversion to biohydrogen. The selected nanomaterial can be used for an effective continuous treatment system for industrial sludge while promoting dark fermentation.

Fire-excluded and frequently burned longleaf pine forests have contrasting soil microbial communities

Prescribed fires are common in forest management, yet we lack a clear picture of how different fire frequencies impact soil systems. Here, we present evidence of microbial community and soil chemistry shifts following sixty years of continuous prescribed fire interval manipulation at the Olustee Experimental Forest in Northeastern Florida. We investigated three fire interval treatments (1 year, 2 years, and 4 years) in addition to an unburned control treatment. We sampled three mineral soil horizons (A, E, and Bh) to elucidate prescribed fire impacts across the soil profile. Our results indicate that only the A horizon was affected by the fire interval manipulations, whereas the deeper E and Bh horizons were minimally impacted. Richness of both bacterial and fungal communities in recurring fire treatments was higher than, and their community composition different from, those in the unburned control in A horizon soils. Similar to the biotic soil attributes, fire interval treatments altered soil chemistry only in the top-most A horizon: the burned treatments had higher total nitrogen, total carbon, phosphorus, and NH4+ than the fire exclusion treatment; the soil chemistry of the deeper E and Bh horizons did not differ among the treatments. All soil chemistry properties correlated with bacterial community composition of the A horizon and nearly all properties correlated with fungal community composition of the A horizon as well, especially when comparing the more frequent burns to the fire exclusion treatment. Indicator taxon analyses identified fire-responsive bacteria and fungi, such as Ktedonobacteria sp. and an unclassified ascomycete that were abundant in the fire exclusion treatment and the ectomycorrhizal Russula spp. that were most abundant in the annual burn treatment. The different fire intervals also impacted fungal guilds, suggesting shifts in community function. The fire exclusion treatment was enriched with ectomycorrhizal, lichenized, and wood saprotrophic fungi, whereas the annual burn treatment was enriched with arbuscular mycorrhizal fungi compared to the other treatments. Our results indicate that long-term changes in the type and amount of detrital inputs and changes in the plant community associated with differing fire frequencies can induce shifts in the soil microbial community.

Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea.

Anaerobic oxidation of methane (AOM) is critical for controlling methane emissions from deep-sea cold seeps. Microbial groups associated with different AOM processes have been briefly investigated, but the AOM activities associated with the utilization of different electron acceptors in the deep-sea methane seeps remain largely unknown. Here, surface sediments (0-4 cm) from two cold seeps (Site F/Haima) and the Xisha trough in the South China Sea (SCS) were incubated to measure AOM potentials driven by nitrite, nitrate, and sulfate as different electron acceptors with isotopically labeled methane gas (13CH4), and the population shifts of microbial communities along the incubation were investigated by high-throughput sequencing and quantitative polymerase chain reaction based on both the 16S rRNA gene and functional genes. Nitrite and nitrate were preferentially used prior to sulfate during the incubation, and nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) contributed more to the methane flux in both the cold seeps and the trough. The highest rates of DAMO and sulfate-dependent anaerobic methane oxidation (SAMO) were detected at Site F, consistent with the transcript abundance of mcrA and dsrB genes during the incubation, and might be explained by the in situ active functional groups. The former process might be explained by Campylobacteria, which could couple sulfide oxidation and nitrate consumption to further participate in the N-DAMO process, while the latter process might be due to the higher proportions of Desulfobacterota. This study elucidates the diversity and potential activities of major microbial groups in the DAMO and SAMO processes in the deep-sea cold seeps using isotopic tracing incubations and provides direct evidence for the occurrence of Nr-/N-DAMO as a previously overlooked microbial methane sink in the deep-sea hydrate-bearing sediments in the SCS. IMPORTANCE Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.

Drivers of pelagic and benthic microbial communities on Central Arctic seamounts

Seamounts are abundant features on the seafloor that serve as hotspots and barriers for the dispersal of benthic organisms. The primary focus of seamount ecology has typically been on the composition and distribution of faunal communities, with far less attention given to microbial communities. Here, we investigated the microbial communities in the water column (0-3400 m depth) and sediments (619-3883 m depth, 0-16 cm below seafloor) along the ice-covered Arctic ridge system called the Langseth Ridge. We contextualized the microbial community composition with data on the benthic trophic state (i.e., organic matter, chlorophyll-a content, and porewater geochemistry) and substrate type (i.e., sponge mats, sediments, basaltic pebbles). Our results showed slow current velocities throughout the water column, a shift in the pelagic microbial community from a dominance of Bacteroidia in the 0-10 m depth towards Proteobacteria and Nitrososphaeria below the epipelagic zone. In general, the pelagic microbial communities showed a high degree of similarity between the Langseth Ridge seamounts to a northern reference site. The only notable differences were decreases in richness between ~600 m and the bottom waters (~10 m above the seafloor) that suggest a pelagic-benthic coupling mediated by filter feeding of sponges living on the seamount summits. On the seafloor, the sponge spicule mats, and polychaete worms were the principal source of variation in sedimentary biogeochemistry and the benthic microbial community structure. The porewater signature suggested that low organic matter degradation rates are accompanied by a microbial community typical of deep-sea oligotrophic environments, such as Proteobacteria, Acidimicrobiia, Dehalococcoidia, Nitrospira, and archaeal Nitrososphaeria. The combined analysis of biogeochemical parameters and the microbial community suggests that the sponges play a significant role for pelagic-benthic coupling and acted as ecosystem engineers on the seafloor of ice-covered seamounts in the oligotrophic central Arctic Ocean.