Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat

Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism

Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD+ through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.

Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic

Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.

Structural and functional analysis of the active cow rumen's microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass

BACKGROUND

Ruminal microbial communities enriched on lignocellulosic biomass have shown considerable promise for the discovery of microorganisms and enzymes involved in digesting cell wall compounds, a key bottleneck in the development of second-generation biofuels and bioproducts, enabling a circular bioeconomy. Cardoon (Cynara cardunculus) is a promising inedible energy crop for current and future cellulosic biorefineries and the emerging bioenergy and bioproducts industries. The rumen microbiome can be considered an anaerobic "bioreactor", where the resident microbiota carry out the depolymerization and hydrolysis of plant cell wall polysaccharides (PCWPs) through the catalytic action of fibrolytic enzymes. In this context, the rumen microbiota represents a potential source of microbes and fibrolytic enzymes suitable for biofuel production from feedstocks. In this study, metatranscriptomic and 16S rRNA sequencing were used to profile the microbiome and to investigate the genetic features within the microbial community adherent to the fiber fractions of the rumen content and to the residue of cardoon biomass incubated in the rumen of cannulated cows.

RESULTS

The metatranscriptome of the cardoon and rumen fibre-adherent microbial communities were dissected in their functional and taxonomic components. From a functional point of view, transcripts involved in the methanogenesis from CO2 and H2, and from methanol were over-represented in the cardoon-adherent microbial community and were affiliated with the Methanobrevibacter and Methanosphaera of the Euryarchaeota phylum. Transcripts encoding glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), and glycoside transferases (GTs) accounted for 1.5% (6,957) of the total RNA coding transcripts and were taxonomically affiliated to major rumen fibrolytic microbes, such as Oscillospiraceae, Fibrobacteraceae, Neocallimastigaceae, Prevotellaceae, Lachnospiraceae, and Treponemataceae. The comparison of the expression profile between cardoon and rumen fiber-adherent microbial communities highlighted that specific fibrolytic enzymes were potentially responsible for the breakdown of cardoon PCWPs, which was driven by specific taxa, mainly Ruminococcus, Treponema, and Neocallimastigaceae.

CONCLUSIONS

Analysis of 16S rRNA and metatranscriptomic sequencing data revealed that the cow rumen microbiome harbors a repertoire of new enzymes capable of degrading PCWPs. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential approach for accelerating the discovery of novel cellulolytic enzymes that could be harnessed for biotechnology. This research contributes a relevant perspective towards degrading cellulosic biomass and providing an economical route to the production of advanced biofuels and high-value bioproducts.

Semi-permeable membrane-covered high-temperature aerobic composting: A review

Semi-permeable membrane-covered high-temperature aerobic composting (SMHC) is a suitable technology for the safe treatment and disposal of organic solid waste as well as for improving the quality of the final compost. This paper presents a comprehensive summary of the impact of semi-permeable membranes centered on expanded polytetrafluoroethylene (e-PTFE) on compost physicochemical properties, carbon and nitrogen transformations, greenhouse gas emission reduction, microbial community succession, antibiotic removal, and antibiotic resistance genes migration. It is worth noting that the semi-permeable membrane can form a micro-positive pressure environment under the membrane, promote the uniform distribution of air in the heap, reduce the proportion of anaerobic area in the heap, improve the decomposition rate of organic matter, accelerate the decomposition of compost and improve the quality of compost. In addition, this paper presents several recommendations for future research areas in the SMHC. This investigation aims to guide for implementation of semi-permeable membranes in high-temperature aerobic fermentation processes by systematically compiling the latest research progress on SMHC.

Microbe combined with Fe2+-heat activated persulfate to decompose phenanthrene in red soil: comparison of acid-resistant degrading microflora and indigenous bacteria

This work is designed to counteract the deficiency of targeted research on the PAHs polluted specific soil, especially when the chemicals extremely denatured it. Phenanthrene-contaminated red soil was treated through two-stage process: persulfate oxidation (on dosages of 3.48%, 5.21%, and 6.94%, combined with Fe2+ and β-cyclodextrin, then heated) followed by biodegradation (indigenous bacteria vs. acid-resistant PAHs-degrading microflora (named ADM)) for 90 days. The dosage of oxidant greatly affected the removal efficiencies, which ranged from 46.78 to 85.34% under different treatment. After undergoing oxidation, the soil pH dropped below 3.0 synchronously and retained relatively strong oxidation state. The indigenous bacteria in red soil showed considerable degradation potential that will not vanish upon the sudden change of soil properties, whose average combined removal reached 95.43%, even higher than subgroups of bioaugmentation, but the population structure showed extremely simplex (Proteobacteria as superior occupied proportion of 91.77% after 90-day rehabilitation). The ADM screened from the coking wastewater was dominated by Klebsiella (75.4%) and Pseudomonas (23.6%), whose cooperation with 6.94% persulfate made the residual PHE reduced to less than 50 mg·kg-1 in about 28 days. High-throughput sequencing analysis showed that the microbial community composition of the ADM applied-group was more abundant in the later stage of remediation. ADM inoculation has the advantages of shortening the restoration period and having a positive impact on the soil micro-ecology.

Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective

Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.

Nitrogen retention and emissions during membrane-covered aerobic composting for kitchen waste disposal

The composting performance and nitrogen transformation during membrane-covered aerobic composting of kitchen waste were investigated. The aerobic composting products of the kitchen waste had a high seed germination index of ∼180%. The application of the membrane increased the mean temperature in the early cooling stage of composting by 4.5℃, resulted in a lower moisture content, and reduced the emissions of NH3 and N2O by 48.5% and 44.1%, respectively, thereby retaining 7.9% more nitrogen in the compost. The adsorption of the condensed water layer under inner-membrane was the reason for reducing NH3 emissions, and finite element modeling revealed that the condensed water layer was present throughout the composting process with a maximum thickness of ∼2 mm in the thermophilic stage. The reduction of N2O emissions was related to the micro-positive pressure in the reactor, which promoted the distribution of oxygen, thus weakening denitrification. In addition, the membrane cover decreased the diversity of the bacterial community and increased the diversity of ammonia-oxidizing strains. This study confirmed that membrane-covered composting was suitable for kitchen waste management and could be used as a strategy to mitigate NH3 and N2O emissions.

Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new?

Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.

Inoculation with thermophiles enhanced the food waste bio-drying and complicated interdomain ecological networks between bacterial and fungal communities

Bio-drying is a practical approach for treating food waste (FW). However, microbial ecological processes during treatment are essential for improving the dry efficiency, and have not been stressed enough. This study analyzed the microbial community succession and two critical periods of interdomain ecological networks (IDENs) during FW bio-drying inoculated with thermophiles (TB), to determine how TB affects FW bio-drying efficiency. The results showed that TB could rapidly colonize in the FW bio-drying, with the highest relative abundance of 5.13%. Inoculating TB increased the maximum temperature, temperature integrated index and moisture removal rate of FW bio-drying (55.7 °C, 219.5 °C, and 86.11% vs. 52.1 °C, 159.1 °C, and 56.02%), thereby accelerating the FW bio-drying efficiency by altering the succession of microbial communities. The structural equation model and IDEN analysis demonstrated that TB inoculation complicated the IDENs between bacterial and fungal communities by significantly and positively affecting bacterial communities (b = 0.39, p < 0.001) and fungal communities (b = 0.32, p < 0.01), thereby enhancing interdomain interactions between bacteria and fungi. Additionally, inoculation TB significantly increased the relative abundance of keystone taxa, including Clostridium sensu stricto, Ochrobactrum, Phenylobacterium, Microvirga and Candida. In conclusion, the inoculation of TB could effectively improve FW bio-drying, which is a promising technology for rapidly reducing FW with high moisture content and recovering resources from it.

Biophotoelectrochemical process co-driven by dead microalgae and live bacteria

Anaerobic reduction processes in natural waters can be promoted by dead microalgae that have been attributed to nutrient substances provided by the decomposition of dead microalgae for other microorganisms. However, previous reports have not considered that dead microalgae may also serve as photosensitizers to drive microbial reduction processes. Here we demonstrate a photoelectric synergistic linkage between dead microalgae and bacteria capable of extracellular electron transfer (EET). Illumination of dead Raphidocelis subcapitata resulted in two-fold increase in the rate of anaerobic bioreduction by pure Geobacter sulfurreducens, suggesting that photoelectrons generated from the illuminated dead microalgae were transferred to the EET-capable microorganisms. Similar phenomena were observed in NO3- reduction driven by irradiated dead Chlorella vulgaris and living Shewanella oneidensis, and Cr(VI) reduction driven by irradiated dead Raphidocelis subcapitata and living Bacillus subtilis. Enhancement of bioreduction was also seen when the killed microalgae were illuminated in mixed-culture lake water, suggesting that EET-capable bacteria were naturally present and this phenomenon is common in post-bloom systems. The intracellular ferredoxin-NADP+-reductase is inactivated in the dead microalgae, allowing the production and extracellular transfer of photoelectrons. The use of mutant strains confirmed that the electron transport pathway requires multiheme cytochromes. Taken together, these results suggest a heretofore overlooked biophotoelectrochemical process jointly mediated by illumination of dead microalgae and live EET-capable bacteria in natural ecosystems, which may add an important component in the energetics of bioreduction phenomena particularly in microalgae-enriched environments.

Martin S, Xie F, Wang J. Continuous-cropping-tolerant soybean cultivars alleviate continuous cropping obstacles by improving structure and function of rhizosphere microorganisms

Introduction

Soybean continuous cropping will change soil microorganisms and cause continuous cropping obstacles, resulting in a significant yield decline. Different soybean cultivars have different tolerances to continuous cropping, but the relationship between continuous cropping tolerance and soil microorganisms is not clear.

Methods

Two soybean cultivars with different tolerances to continuous cropping were used to study the effects of continuous cropping on soil physical and chemical properties, nitrogen and phosphorus cyclic enzyme activities, rhizosphere soil microbial community and function.

Results

The results showed that the yield reduction rate of a continuous-cropping-tolerant cultivar (L14) was lower than that of a continuous-cropping-sensitive cultivar (L10) under continuous cropping. At R1 and R6 growth stages, soil nutrient content (NH₄ ⁺-N, NO₃ ^--N, AP, DOM, TK, and pH), nitrogen cycling enzyme (URE, NAG, LAP) activities, phosphorus cycling enzyme (ALP, NPA, ACP) activities, copy numbers of nitrogen functional genes (AOA, AOB, nirK, nirK) and phosphorus functional genes (phoA, phoB) in L14 were higher than those in L10. Soybean cultivar was an important factor affecting the structure and functional structure of bacterial community under continuous cropping. The relative abundances of Proteobacteria, Bacteroidota, Acidobacteriota and Verrucomicrobiota with L14 were significantly higher than those of L10. The complexity of the soil bacterial community co-occurrence network in L14 was higher than that in L10.

Discussion

The continuous-cropping-tolerant soybean cultivar recruited more beneficial bacteria, changed the structure and function of microbial community, improved soil nitrogen and phosphorus cycling, and reduced the impact of continuous cropping obstacles on grain yield.

Mixed-litter effects of fresh leaf semi-decomposed litter and fine root on soil enzyme activity and microbial community in an evergreen broadleaf karst forest in southwest China

Litter decomposition is the main process that affects nutrient cycling and carbon budgets in mixed forests. However, knowledge of the response of the soil microbial processes to the mixed-litter decomposition of fresh leaf, semi-decomposed leaf and fine root is limited. Thus, a laboratory microcosm experiment was performed to explore the mixed-litter effects of fresh leaf, semi-decomposed leaf and fine root on the soil enzyme activity and microbial community in an evergreen broadleaf karst forest in Southwest China. Fresh leaf litter, semi-decomposed litter and fine root in the Parakmeria nitida and Dayaoshania cotinifolia forests, which are unique protective species and dominant species in the evergreen broadleaf forest, were decomposed alone and in all possible combinations, respectively. Our results showed that the mass loss of fresh leaf litter in three mixed-litter treatment was significantly higher than that in two mixed-litter treatment in the P. nitida and D. cotinifolia forests. Mass loss of fine root in the single litter treatment was significantly lower in the P. nitida forest and higher in the D. cotinifolia forest compared to that in the other litter treatments. There were insignificant differences in the activities of β-glucosidase (BG) and leucine aminopeptidase (LAP) between control and mixed-litter treatment in the P. nitida forest and between control and single litter treatment in the D. cotinifolia forest. The N-acetyl-β-D-glucosaminidase (NAG) activity was significantly increased by the single litter decomposition of fresh leaf and fine root and three mixed-litter decomposition in the P. nitida and D. cotinifolia forests. The activity of acid phospomonoesterase (AP) in the decomposition of fresh leaf litter was lower in the P. nitida forest and higher in the D. cotinifolia forest compared to that in control. The most dominant soil bacteria were Proteobacteria in the P. nitida forest and were Actinobacteria and Proteobacteria in the D. cotinifolia forest. Shannon, Chao1, ACE and PD indexes in the mixed-litter decomposition of fresh leaf and semi-decomposition litter were higher than that in control in P. nitida forest. There were insignificant differences in observed species and indexes of Chao1, ACE and PD between litter treatments in the D. cotinifolia forest. Richness of mixed-litter significantly affected mass loss, soil enzyme activity and microbial diversity in the P. nitida forest. Litter N concentration and the presence of fresh leaf litter were significantly correlated with the mass loss and soil enzyme activity in the P. nitida and D. cotinifolia forests. These results indicated that the presence of fresh leaf litter showed a non-negligible influence on mixed-litter decomposition and soil enzyme activity, which might be partly explained by litter initial quality in the P. nitida and D. cotinifolia forests.

Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost

Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.

Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82T

Acidisarcina polymorpha SBC82T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82T and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82T by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82T was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.

Responses of Rhizosphere Bacterial and Fungal Communities to the Long-Term Continuous Monoculture of Water Oat

As an cultivated aquatic vegetable, the long-term continuous monocropping of water oat results in the frequent occurrence of diseases, the deterioration of ecological system and decreased quality of water oat. In this study, real-time quantitative PCR (qPCR) and Illumina high-throughput sequencing were used to determine the dynamic changes in bacterial and fungal communities in rhizosphere soil under continuous cropping of water oat for 1, 5, 10, 15 and 20 years (Y1, Y5, Y10, Y15 and Y20), and soil properties and enzyme activities were also determined. Results showed that the contents of soil organic carbon (SOC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP) and the activities of four soil enzymes increased in Y5 and Y10 and then decreased in Y15 and Y20. Spearman correlation analysis identified SOC, TN, AP and AN as the main factors that affect the four enzyme activities. The qPCR results showed that there was no significant difference in bacterial abundance between the different planting years, while the fungal abundance first increased and then decreased. The long-term continuous planting of water oat (Y15 and Y20) significantly reduced the operational taxonomic unit numbers and the Shannon, Chao1, and ACE indices of rhizosphere bacteria and fungi. The bacterial and fungal community compositions were markedly affected by the continuous planting year. The relative abundances of Bacteroidetes and Firmicutes decreased significantly in Y10 and Bacteroidetes increased significantly in Y15. Relative abundances of dominated Mortierellomycota and Ascomycota phyla increased with the continuous cropping years, while Rozellomycota presented the opposite trend. The AK, AN, and SOC were the main factors that changed the bacterial community, while AK and AP significantly shifted the fungal community. Thus, long-term continuous planting of water oat resulted in the deterioration of soil nutrients and microbial communities. The results provided a reference for the remediation of soil under continuous water oat planting and sustainable development of water oat industry.

Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high-yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.

The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems

Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.

Long-term warming effects on the microbiome and nifH gene abundance of a common moss species in sub-Arctic tundra

Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of moss microbiomes in these environments. Here, we studied the total and potentially active bacterial communities associated with Racomitrium lanuginosum in response to a 20-yr in situ warming in an Icelandic heathland. We evaluated the effect of warming and warming-induced shrub expansion on the moss bacterial community composition and diversity, and nifH gene abundance. Warming changed both the total and the potentially active bacterial community structure, while litter abundance only affected the total bacterial community structure. The abundance of nifH genes was negatively affected by litter abundance. We also found shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and noncyanobacterial diazotrophs increasing in relative abundance. Our data suggest that the moss microbial community and potentially nitrogen fixing taxa will be sensitive to future warming, partly via changes in litter and shrub abundance.

Analysis of the influence paths of land use and landscape pattern on organic matter decomposition in river ecosystems: Focusing on microbial groups

Organic matter decomposition (OMD) is one of the important river ecosystem functions. Changes in land use and landscape pattern (LULP) have a serious influence on the OMD in neighboring river ecosystems. However, there is limited information on the influence paths of LULP on organic matter decomposition in river ecosystems. In this study, cotton strip (CS) as a substitute for investigating OMD, was introduced to the delineated catchments in Luanhe River Basin in China, meanwhile combining with remote sensing interpretation, water quality analysis, microbial sequencing, and redundancy analysis (RDA) to identify the dominant LULP metrics, water quality parameters, and microbial groups controlling the OMD. Then the structural equation models (SEMs) were used to connect these dominant controlling factors to track the influence paths of LULP on OMD in river ecosystems. RDA results indicated that construction land (CON), farmland (FAR) and landscape shape index (LSI) in LULP, total nitrogen (TN), chemical oxygen demand (COD) and pH in water quality, bacterial phyla Planctomycetes and Firmicutes, as well as fungal phyla Chytridiomycota and Basidiomycota were the dominant factors controlling the OMD (quantified by tensile strength loss (TSL) and respiration (RES)). These four microbial phyla contributed significantly to OMD. SEMs further proposed three paths to explain the mechanism of LULP influencing on OMD, which were CON - TN - Firmicutes - TSL, CON - TN - Chytridiomycota - RES, and FAR - COD - Chytridiomycota - TSL. CON promoted OMD mainly through enhancing TN content in river water to increase Firmicutes and Chytridiomycota. FAR increased Chytridiomycota by decreasing COD in river water, promoting OMD. These results will deepen our understanding of the influence of LULP on river ecosystem functions and provide valuable information for policymakers and managers to carry out watershed land planning and river management in the future.

Impact of fumigants on non-target soil microorganisms: a review

Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.

Effect of lignin on short-chain fatty acids production from anaerobic fermentation of waste activated sludge

Lignin, a biological resource with great potential, can be as high as ∼16% of the total organics in the waste activated sludge (WAS). This work therefore aims to fill the knowledge gap about the effect of lignin on short-chain fatty acids (SCFAs) production from anaerobic fermentation of sludge. Experimental results showed that lignin promoted rather than inhibited SCFAs production. Specifically, the presence of 15% lignin promoted the SCFAs production from 129.1 ± 6.5 to 223.14 ± 7.8 mg COD/g VSS compared with the control, and the proportion of acetic increased by 61.8%, while that of propionic decreased by 44.9%. Mechanism exploration revealed that lignin improved the solubilization of biodegradable substrates due to its hydrophobic characteristics. In addition, lignin enhanced the acidogenesis process, possibly by perfecting the electron transfer chain in the fermentation system, and the quinone structure in lignin may compete electrons with methanogens to inhibit the consumption of SCFAs. Microbiological analysis showed that the abundance of microorganisms related to acidogenesi, especially the acetogenesis, including Proteiniclasticum sp., Acetoanaerobium sp., in the fermenter with lignin increased, which caused the community to shift towards specialized and diverse SCFAs production.

Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale

Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.

Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels

Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.

Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.

Effect of biochar combined with a biotrickling filter on deodorization, nitrogen retention, and microbial community succession during chicken manure composting

The high-nitrogen content and dense structure of poultry manure compost cause volatilization of N to ammonia (NH₃). This study evaluated the combined application of biochar and biotrickling filtration (BTF) to remove of odor in chicken manure mixed straw compost (w/w, 2.5:1). Adding of 10% biochar reduced NH₃, hydrogen sulfide (H₂S), and total volatile organic compounds (TVOCs) contents by 20.04%, 16.18%, and 17.55% respectively, and decreased the N loss rate by 8.27%, compared with those observed in control. The organic matter content decreased by 28.11% and germination index reached 97.36% in the experimental group. Meanwhile, the N-cycling microorganisms such as Pusillimonas and Pseudomonas became more active, and the relative abundance of sulfur-cycling microorganisms Hydrogenispora decreased in the experimental group. Following BTF application, the NH₃, H₂S, and TVOCs removal rates reached 95%, 97%, and 53%, respectively.

Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China

In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.

Development of a consortium-based microbial agent beneficial to composting of distilled grain waste for Pleurotus ostreatus cultivation

BACKGROUND

Pleurotus ostreatus is an edible mushroom popularly cultivated worldwide. Distilled grain waste (DGW) is a potential substrate for P. ostreatus cultivation. However, components in DGW restrict P. ostreatus mycelial growth. Therefore, a cost-effective approach to facilitate rapid P. ostreatus colonization on DGW substrate will benefit P. ostreatus cultivation and DGW recycling.

RESULTS

Five dominant indigenous bacteria, Sphingobacterium sp. X1, Ureibacillus sp. X2, Pseudoxanthomonas sp. X3, Geobacillus sp. X4, and Aeribacillus sp. X5, were isolated from DGW and selected to develop a consortium-based microbial agent to compost DGW for P. ostreatus cultivation. Microbial agent inoculation led to faster carbohydrate metabolism, a higher temperature (73.2 vs. 71.2 °C), a longer thermophilic phase (5 vs. 3 days), and significant dynamic changes in microbial community composition and diversity in composts than those of the controls. Metagenomic analysis showed the enhanced microbial metabolisms, such as xenobiotic biodegradation and metabolism and terpenoid and polyketide metabolism, during the mesophilic phase after microbial agent inoculation, which may facilitate the fungal colonization on the substrate. In accordance with the bioinformatic analysis, a faster colonization of P. ostreatus was observed in the composts with microbial inoculation than in control after composting for 48 h, as indicated from substantially higher fungal ergosterol content, faster lignocellulose degradation, and higher lignocellulase activities in the former than in the latter. The final mushroom yield shared no significant difference between composts with microbial inoculation and control, with 0.67 ± 0.05 and 0.60 ± 0.04 kg fresh mushroom/kg DGW, respectively (p > 0.05).

CONCLUSION

The consortium-based microbial agent comprised indigenous microorganisms showing application potential in composting DGW for providing substrate for P. ostreatus cultivation and will provide an alternative to facilitate DGW recycling.

Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

Simple Summary

Tropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.

Abstract

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

Complete genome sequence of the cellulolytic planctomycete Telmatocola sphagniphila SP2T and characterization of the first cellulolytic enzyme from planctomycetes

Planctomycetes of the family Gemmataceae are strictly aerobic chemo-organotrophs that display a number of hydrolytic capabilities. A member of this family, Telmatocola sphagniphila SP2^T, is the first described planctomycete with experimentally proven ability for growth on cellulose. In this study, the complete genome sequence of strain SP2^T was obtained and the genome-encoded determinants of its cellulolytic potential were analyzed. The T. sphagniphila SP2^T genome was 6.59 Mb in size and contained over 5200 potential protein-coding genes. The search for enzymes that could be potentially involved in cellulose degradation identified a putative cellulase that contained a domain from the GH44 family of glycoside hydrolases. Homologous enzymes were also revealed in the genomes of two other Gemmataceae planctomycetes, Zavarzinella formosa A10^T and Tuwongella immobilis MBLW1^T. The gene encoding this predicted cellulase in strain SP2^T was expressed in E. coli and the hydrolytic activity of the recombinant enzyme was confirmed in tests with carboxymethyl cellulose but not with crystalline cellulose, xylan, mannan or laminarin. This is the first experimentally characterized cellulolytic enzyme from planctomycetes.

Patterns of heavy metal resistant bacterial community succession influenced by biochar amendment during poultry manure composting

The purpose of this study was to investigate the heavy metal resistant bacteria (HMRB) community succession and bacterial activity in poultry manure (PM) composting. Five different concentration of chicken manure biochar (CMB) at 0%, 2%, 4%, 6%, and 10% on a dry weight basis was applied with initial feedstock (poultry manure + wheat straw) and indicated with T1, T2, T3, T4, and T5. In addition, high-throughput sequencing, principal coordinate analysis, and correlation analysis were used to analyze the evolution of HMRB communities during composting. The study indicated that crucial phyla were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The bacterial diversity in the CMB amendment treatment was higher than in the control treatment, and T4 treatment has the highest among all CMB applied treatments. Moreover, results from CCA indicated that T4 and T5 treatments quickly enters the high-temperature period which is maintained for 5 days, and is significantly positively correlated with Proteobacteria, and Actinobacteria. These findings offer insight into potential strategies to understand the succession of HMRBs during PM reuse. Overall, the above results show the addition of 6% biochar (T4) was potentially beneficial to enrich the abundance of bacterial community to improve composting environment quality and composting efficiency. In addition, effective to immobilized the heavy metals and HMRB in the end product.

Responses of Root Endophytes to Phosphorus Availability in Peach Rootstocks With Contrasting Phosphorus-Use Efficiencies

Phosphorus (P) is an important macronutrient for all lives, but it is also a finite resource. Therefore, it is important to understand how to increase the P availability and plant uptake. The endophytes can help host plants to improve P uptake and will be apparently affected by plant genotypes. To investigate the mechanism of root endophytes in promoting P uptake of peach rootstocks, we analyzed the variations of the root endophytic fungal and bacterial communities of peach rootstocks with different P efficiencies under high or low level of P addition. Results showed that Proteobacteria was the dominant bacterial phylum in the roots of all rootstocks under the two levels of P addition. At low P level, the abundance of Actinoplanes in phosphorus-inefficiency root system was apparently higher than that at high P level. Actinoplanes produced important secondary metabolites, improving the stress resistance of plants. Under high P condition, the abundance of Ferrovibrio was higher in Qing Zhou Mi Tao than in Du Shi. Fe oxides considerably reduced the availability of applied P, which partially explained why the P utilization in Qing Zhou Mi Tao is inefficient. Further, Ascomycota was the dominant fungal phylum in the roots of all rootstocks under different levels of P addition. The fungi community of roots varied in different rootstocks at each P level, but was similar for the same rootstock at different P levels, which indicated that genotype had a greater effect than P addition on the fungal community of peach rootstocks.

Decomposition of peatland DOC affected by root exudates is driven by specific r and K strategic bacterial taxa

In peatlands, decomposition of organic matter is limited by harsh environmental conditions and low decomposability of the plant material. Shifting vegetation composition from Sphagnum towards vascular plants is expected in response to climate change, which will lead to increased root exudate flux to the soil and stimulation of microbial growth and activity. We aimed to evaluate the effect of root exudates on the decomposition of recalcitrant dissolved organic carbon (DOC) and to identify microorganisms involved in this process. The exudation was mimicked by an addition of a mixture of ¹³C labelled compounds into the recalcitrant DOC in two realistic levels; 2% and 5% of total DOC and peatland porewater with added root exudates was incubated under controlled conditions in the lab. The early stage of incubation was characterized by a relative increase of r-strategic bacteria mainly from Gammaproteobacteria and Bacteriodetes phyla within the microbial community and their preferential use of the added compounds. At the later stage, Alphaproteobacteria and Acidobacteria members were the dominating phyla, which metabolized both the transformed ¹³C compounds and the recalcitrant DOC. Only higher exudate input (5% of total DOC) stimulated decomposition of recalcitrant DOC compared to non-amended control. The most important taxa with a potential to decompose complex DOC compounds were identified as: Mucilaginibacter (Bacteriodetes), Burkholderia and Pseudomonas (Gammaproteobacteria) among r-strategists and Bryocella and Candidatus Solibacter (Acidobacteria) among K-strategists. We conclude that increased root exudate inputs and their increasing C/N ratio stimulate growth and degradation potential of both r-strategic and K-strategic bacteria, which make the system more dynamic and may accelerate decomposition of peatland recalcitrant DOC.

Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China

Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.

Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria

BACKGROUND

Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem.

RESULTS

Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens.

CONCLUSIONS

The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.

Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China

The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (August and November in 2017 and May 2018) with a gradient of water table changes and temperatures at the Dajiuhu peatland, Central China. The samples were analyzed with 16S rRNA high-throughput sequencing and Biolog EcoMicroplates. Bacterial communities varied in the relative abundances of dominant taxa and harbored exclusive indicator operational taxonomic units across the different months. Despite these differences, bacterial communities showed high similarities in carbon utilization, with preferences for esters (pyruvic acid methyl ester, Tween 40, Tween 80, and D-galactonic acid γ-lactone), amino acids (L-arginine and L-threonine), and amines (phenylethylamine and putrescine). However, rates of carbon utilization (as indicated by average well-color development) and metabolic diversity (McIntosh and Shannon index) in May and August were higher than those in November. Redundancy analysis revealed that the seasonal variations in bacterial communities were significantly impacted by the level of the water table, whereas the temperature had a fundamental role in bacterial carbon utilization rate. Co-occurrence analysis identified Sphingomonas, Mucilaginibacter, Novosphingobium, Lacunisphaera, Herminiimonas, and Bradyrhizobium as keystone species, which may involve in the utilization of organic compounds such as amino acids, phenols, and others. Our findings suggest that bacterial community functions were more stable than their compositions in the context of water table changes. These findings significantly expand our current understanding of the variations of bacterial community structures and metabolic functions in peatland ecosystems in the context of global warming and fluctuation of the water table.

Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.

Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands

Tropical coastal wetlands provide a range of ecosystem services that are closely associated with microbially-driven biogeochemical processes. Knowledge of the main players and their drivers in those processes can have huge implications on the carbon and nutrient fluxes in wetland soils, and thus on the ecosystems services we derive from them. Here, we collected surface (0-5 cm) and subsurface (20-25 cm) soil samples along a transect from forested freshwater wetlands, to saltmarsh, and mangroves. For each sample, we measured a range of abiotic properties and characterised the diversity of bacterial communities using 16S rRNA gene amplicon sequencing. The alpha diversity of bacterial communities in mangroves exceeded that of freshwater wetlands, which were dominated by members of the Acidobacteria, Alphaproteobacteria and Verrucomicrobia, and associated with high soil pore-water concentrations of soluble reactive phosphorous, and nitrogen as nitrate and nitrite (N-NO_X^-). Bacterial communities in the saltmarsh were strongly stratified by depth and included members of the Actinobacteria, Chloroflexi, and Deltaproteobacteria. Finally, the mangroves were dominated by representatives of Deltaproteobacteria, mainly Desulfobacteraceae and Synthrophobacteraceae, and were associated with high salinity and soil pore-water concentrations of ammonium (N-NH₄⁺). These communities suggest methane consumption in freshwater wetlands, and sulfate reduction in deep soils of marshes and in mangroves. Our work contributes to the important goal of describing reference conditions for specific wetlands in terms of both bacterial communities and their drivers. This information may be used to monitor change and assess wetland health and function.

The interplay of labile organic carbon, enzyme activities and microbial communities of two forest soils across seasons

Soil labile organic carbon (LOC) responds rapidly to environmental changes and plays an important role in carbon cycle. In this study, the seasonal fluctuations in LOC, the activities of carbon-cycle related enzymes, and the bacterial and fungal communities were analyzed for soils collected from two forests, namely Betula albosinensis (Ba) and Picea asperata Mast. (Pa), in the Qinling Mountains of China. Results revealed that the seasonal average contents of microbial biomass carbon (MBC), easily oxidized organic carbon (EOC), and dissolved organic carbon (DOC) of Pa forest soil were 13.5%, 30.0% and 15.7% less than those in Ba soil. The seasonal average enzyme activities of β-1,4-glucosidase (βG), and β-1,4-xylosidase (βX) of Ba forest soils were 30.0% and 32.3% higher than those of Pa soil while the enzyme activity of cellobiohydrolase (CBH) was 19.7% lower. Furthermore, the relative abundance of Acidobacteria was significantly higher in summer than in winter, whereas the relative abundance of Bacteroidetes was higher in winter. Regarding the fungal communities, the relative abundance of Basidiomycota was lowest in winter, whereas Ascomycota predominated in the same season. In addition, the soil LOC was significantly positively correlated with the CBH, βG and βX activities. Changes in LOC were significantly correlated with Acidobacteria, Bacteroidetes and Basidiomycota. We conclude that the seasonal fluctuations in forest soil LOC fractions relied on carbon cycle-associated enzymatic activities and microorganisms, which in turn were affected by climatic conditions.

Hydroxyapatite as a passivator for safe wheat production and its impacts on soil microbial communities in a Cd-contaminated alkaline soil

The remediation of Cd-contaminated alkaline soil plays a critical role in safe wheat production. In this study, hydroxyapatite (HAP), a functional environmental remediation material, was selected to investigate the effects of HAP on cadmium accumulation in winter wheat (Triticum aestivum L.), Cd bioavailability in alkaline soil moderately polluted with Cd (2.46 mg kg^-1) and the soil bacterial community via pot experiments. The results showed HAP effectively inhibited Cd accumulation in the grains of two investigated wheat cultivars by hindering root uptake. The Cd concentrations decreased by 49.9-81.9%, and 35.7-92.4% in the grains of Zhoumai-30 and Zhengmai-7698, respectively. HAP increased the soil pH and reduced the bioavailability of Cd. 16S rRNA sequencing analysis indicated that the changes of soil physicochemical properties changed the diversity and composition of the bacterial community by increasing the relative abundance of beneficial soil bacteria. These results demonstrated the application of 2.5% HAP combined with planting Zhengmai-7698 treatment was a potential remediation method for safe wheat production, and also benefited soil P and N cycling by increasing the relative abundance of beneficial bacteria. The good performance of HAP in inhabiting Cd accumulation in wheat grains indicated it is a promising material for safe wheat production.

Trimethylornithine Membrane Lipids: Discovered in Planctomycetes and Identified in Diverse Environments

Intact polar membrane lipids (IPLs) are the building blocks of all cell membranes. There is a wide range of phosphorus-free IPL structures, including amino acid containing IPLs, that can be taxonomically specific. Trimethylornithine membrane lipids (TMOs) were discovered in northern wetland Planctomycete species that were isolated and described in the last decade. The trimethylated terminal nitrogen moiety of the ornithine amino acid in the TMO structure gives the lipid a charged polar head group, similar to certain phospholipids. Since their discovery, TMOs have been identified in various other recently described northern latitude Planctomycete species, and in diverse environments including tundra soil, a boreal eutrophic lake, meso-oligotrophic lakes, and hot springs. The majority of environments or enrichment cultures in which TMOs have been observed include predominately heterotrophic microbial communities involved in the degradation of recalcitrant material and/or low oxygen methanogenic conditions at primarily northern latitudes. Other ecosystems occupied with microbial communities that possess similar metabolic pathways, such as tropical peatlands or coastal salt marshes, may include TMO producing Planctomycetes as well, further allowing these lipids to potentially be used to understand microbial community responses to environmental change in a wide range of systems. The occurrence of TMOs in hot springs indicates that these unique lipids could have broad environmental distribution with different specialized functions. Opportunities also exist to investigate the application of TMOs in microbiome studies, including forensic necrobiomes. Further environmental and microbiome lipidomics research involving TMOs will help reveal the evolution, functions, and applications of these unique membrane lipids.

Contrasting bacterial communities and their assembly processes in karst soils under different land use

Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and multivariate statistical analysis. Bacterial communities and functions remarkably distinguished between soils under different land use. Both edaphic properties (the content of SO₄^2-, C/N, pH, TN) and weathering processes, such as Si concentration, Mg/Al and Ca/Al, significantly impacted on soil bacterial community structures. Variable selections were predominant ecological processes, and pH and SO₄^2- concentration were of significance in community assembly. Random molecular ecological network analysis revealed a more stable and complex microbial network in the forest ecosystem, which can quickly response to environmental change. Forest soil bacteria were mainly phototrophs, involving in C and N cycles, whereas those in arable soils were mainly chemoheterotrophs, capable of degrading organic fertilizers due to anthropogenic activities as confirmed by the analysis of keystone taxa, indicators and functional prediction. These results reveal that land use constructed soil bacterial communities in different aspects such as the structure, potential functions, microbial interactions and correlations with environmental variables. To our knowledge, this is the first report on bacterial community assembly in karst soils under different land use which enhances our understanding about how land use impact on microbial interaction and community assembly processes.

Effect of excess sludge and food waste feeding ratio on the nutrient fractions, and bacterial and fungal community during aerobic co-composting

The effect of excess sludge and food waste feeding ratio on the co-composting process was explored using 5% bagasse biochar as an additive and conditioner. Results showed that when the mass ratio was 1:1, nitrogen fixation ability was the strongest and ammonia nitrogen increment in the pile reached 2.31 mg/g. The increase in excess sludge content/food waste ratio during composting was conducive to the accumulation of H₂O-P, BD-P, HCl-P, NaOH-P and NaOH₈₅-P. When the ratio of excess sludge to food waste mass was 1:1, the relative abundance of Firmicutes was the largest in the compost, which corresponded to 72.77% at the phylum level. Food waste mass was more beneficial to the growth and reproduction of microorganisms and to the metabolic activities related to membrane transport. Considering the fungal content, Ascomycota and Basidiomycota were maximum, with relative abundance of 69.53% and 20.91%, respectively, at the mass ratio of 1:1.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Beneficial Effects of Mixing Kentucky Bluegrass With Red Fescue via Plant-Soil Interactions in Black Soil of Northeast China

Continuous monoculture of cool-season turfgrass causes soil degradation, and visual turf quality decline is a major concern in black soil regions of Northeast China. Turf mixtures can enhance turfgrass resistance to biotic and abiotic stresses and increase soil microbial diversity. Understanding mechanism by plant-soil interactions and changes of black soil microbial communities in turf mixture is beneficial to restoring the degradation of urbanized black soils and maintaining sustainable development of urban landscape ecology. In this study, based on the previous research of different sowing models, two schemes of turf monoculture and mixture were conducted in field plots during 2016-2018 in a black soil of Heilongjiang province of Northeast China. The mixture turf was established by mixing 50% Kentucky bluegrass "Midnight" (Poa pratensis L.) with 50% Red fescue "Frigg" (Festuca rubra L.); and the monoculture turf was established by sowing with pure Kentucky bluegrass. Turf performance, soil physiochemical properties, and microbial composition from rhizosphere were investigated. Soil microbial communities and abundance were analyzed by Illumina MiSeq sequencing and quantitative PCR methods. Results showed that turfgrass quality, turfgrass biomass, soil organic matter (SOM), urease, alkaline phosphatase, invertase, and catalase activities increased in PF mixture, but disease percentage and soil pH decreased. The microbial diversity was also significantly enhanced under turf mixture model. The microbial community compositions were significantly different between the two schemes. Turf mixtures obviously increased the abundances of Beauveria, Lysobacter, Chryseolinea, and Gemmatimonas spp., while remarkably reduced the abundances of Myrothecium and Epicoccum spp. Redundancy analysis showed that the compositions of bacteria and fungi were related to edaphic parameters, such as SOM, pH, and enzyme activities. Since the increasing of turf quality, biomass, and disease resistance were highly correlated with the changes of soil physiochemical parameters and microbial communities in turf mixture, which suggested that turf mixture with two species (i.e., Kentucky blue grass and Red fescue) changed soil microbial communities and enhanced visual turfgrass qualities through positive plant-soil interactions by soil biota.

Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types

Background:

The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types.

Objective:

In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil.

Methods:

A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level.

Result:

Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens.

Conclusion:

Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient

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

Cell-Free Fermentation Broth of Bacillus velezensis Strain S3-1 Improves Pak Choi Nutritional Quality and Changes the Bacterial Community Structure of the Rhizosphere Soil

Bacillus velezensis is a plant growth-promoting rhizobacteria (PGPR) that has long been proven to improve the growth of plants, and it has been widely used in agriculture. However, in many reports, we observed that during the application of bacterial fluids, it appeared that the effect of the cell-free fermentation broth (CFB) was ignored. The purpose of this study is to compare the effect of the no inoculation treatment (CK), the B. velezensis strain S3-1 treatment (S), the CFB treatment in the Pak choi, soil bacterial community structure, soil enzyme activity, and field soil properties. The results have shown that, compared to the inoculation B. velezensis strain S3-1 treatment and the no-inoculation treatment; the inoculation of the CFB treatment can significantly enhance the soluble protein, soluble solids, ascorbic acid of Pak choi and increase the total phosphorus content and electrical conductivity (EC) in the soil. Based on high-throughput sequencing data, our analysis of soil microbial communities used R, NETWORK, and PICRUSt showed that the CFB treatment can enhance the relative abundance of Acidobacteria in the soil, decrease the abundance of native Bacillus in the soil, change the microbial community structure of the top 50 operational taxonomic units (OTUs), and improve soil microbial carbon metabolism and nitrogen metabolism. Overall, we observed that CFB treatment can also improve plant nutrition and change soil microbial communities. This study provides new insights for the application of microbial fertilizers in agricultural production.

Seasonal Microbial Community Characteristic and Its Driving Factors in a Copper Tailings Dam in the Chinese Loess Plateau

A combined soil bacterial and fungal community survey was conducted for a copper tailings dam in the Chinese Loess Plateau. We investigated the seasonal differences in the composition and function of soil microbial community to examine the key environmental factors influencing soil microorganisms during restorative ecological processes. Significant seasonal differences were found in the community structure of both bacterial and fungal communities. Bacterial community abundance and fungal community (Shannon index) measurements were highest in summer. Soil nitrite nitrogen (NO₂ ^--N) was the dominant factor influencing both bacterial and fungal communities. The bacterial community composition was significantly affected by NO₂ ^--N and ammonium nitrogen (NH₄ ⁺-N) in spring, and fungal community structure was significantly affected by soil water content in autumn. Moreover, the fungal community exhibited significant functional feature differences among seasons, whereas bacterial community functional groups remained similar. This study aimed to clarify the adaptation response of microbes applying different approaches used in ecological restoration approaches specific to mining areas, and to identify the natural biofertility capacity of the microbial communities that colonize soil ecosystems.

Successive mineral nitrogen or phosphorus fertilization alone significantly altered bacterial community rather than bacterial biomass in plantation soil

Bacteria play determining roles in forest soil environment and contribute to essential functions in the cycling of nitrogen (N) and phosphorus (P). Understanding the effects of different fertilizer applications, especially successive fertilization, on soil properties and bacterial community could reveal the impacts of fertilization on forest soil ecology and shed light on the nutrient cycling in forest system. This study aimed to evaluate the impacts of successive mineral N (NH₄NO₃) and P (NaH₂PO₄) fertilization at different rates, alone or together, on soil bacterial biomass and communities at 0-5, 5-10, and 10-20 cm. Compared with the control, N fertilization decreased soil pH, but P alone or with N fertilization had negligibly negative impacts on soil pH. Different mineral fertilizer applications, alone or together, showed no significant effects on soil organic matter contents, relative to the control treatment. Bacterial biomass remained stable to different fertilizations but decreased with sampling depths. Sole N or P fertilization, rather than combined fertilizations, significantly changed soil bacterial community structures. Our results demonstrated that mineral N or P fertilization alone significantly affected bacterial community structures rather than biomass in the plantation soils. KEY POINTS: • Impacts of successive mineral fertilization on soil bacteria were determined. • Mineral fertilization showed negligible impacts on bacterial biomass. • N additions stimulated Chloroflexi relative abundances. • Mineral N or P fertilization significantly altered bacterial community structure.

Bacterial succession in epiphytic biofilms and deciduous layer sediments during Hydrilla verticillata decay: A field investigation

Submersed macrophytes decay is an important natural process and has important role in mass and energy flow in aquatic ecosystems. However, little is known about the dynamical changes in nutrients release and bacterial community during submersed macrophyte decay in natural environment. In this study, a field observation was conducted in a wetland dominated with Hydrilla verticillata for 36 days. Increase of H₂O₂ and malondialdehyde (MDA) content and decrease of soluble proteins concentration were detected in leaves during H. verticillata decay. Meanwhile, ammonium-N, soluble microbial products (SMP) and TOC concentration increased in overlying water. According to bacterial 16S rRNA Illumina sequencing analysis, the Shannon values were lower in epiphytic biofilms than deciduous layer sediments. The relative abundances of Proteobacteria, Cyanobacteria and Actinobacteria were higher in epiphytic biofilms than in deciduous layer sediments (P < 0.05). Co-occurrence network analyses showed that a total of 578 and 845 pairs of correlations (|r| > 0.6) were identified from 122 and 112 genera in epiphytic biofilms and deciduous layer sediments, respectively. According to co-occurrence patterns, eight hubs were mainly from phyla Proteobacteria, Acidobacteria and Parcubacteria in epiphytic biofilms; while 37 hubs from the 14 phyla (Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, et al.) were detected in deciduous layer sediments. Our results indicate that bacterial community in deciduous layer sediments was more susceptible than in epiphytic biofilms during decay process. These data highlight the role of microbial community in deciduous layer sediments on nutrients removal during H. verticillata decay and will provide useful information for wetland management.