Soil microbial identity explains home-field advantage for litter decomposition

Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.

Fast Bacterial Succession Associated with the Decomposition of Larix gmelinii Litter in Wudalianchi Volcano

In order to understand the role of microorganisms in litter decomposition and the nutrient cycle in volcanic forest ecosystems, the dominant forest species Larix gmelinii in the volcanic lava plateau of the Wudalianchi volcano was considered as the research object. We analyzed the response of bacterial community structure and diversity to litter decomposition for 1 year, with an in situ decomposition experimental design using litter bags and Illumina MiSeq high-throughput sequencing. The results showed that after 365 days, the litter quality residual rate of Larix gmelinii was 77.57%, and the litter N, P, C:N, C:P, and N:P showed significant differences during the decomposition period (p < 0.05). The phyla Cyanobacteria and the genus unclassified_o_Chloroplast were the most dominant groups in early decomposition (January and April). The phyla Proteobacteria, Actinobacteriota, and Acidobacteriota and the genera Massilia, Pseudomonas, and Sphingomona were higher in July and October. The microbial communities showed extremely significant differences during the decomposition period (p < 0.05), with PCoa, RDA, and litter QRR, C:P, and N as the main factors driving litter bacteria succession. Microbial functional prediction analysis showed that Chloroplasts were the major functional group in January and April. Achemoheterotrophy and aerobic chemoheterotrophy showed a significant decrease as litter decomposition progressed.

Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective

Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.

Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production

Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.

Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species

Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.

Unrevealing the potential of microbes in decomposition of organic matter and release of carbon in the ecosystem

Organic matter decomposition is a biochemical process with consequences affecting climate change and ecosystem productivity. Once decomposition begins, C is lost as CO2 or sequestered into more recalcitrant carbon difficult to further degradation. As microbial respiration releases carbon dioxide into the atmosphere, microbes act as gatekeepers in the whole process. Microbial activities were found to be the second largest CO2 emission source in the environment after human activities (industrialization), and research investigations suggest that this may have affected climate change over the past few decades. It is crucial to note that microbes are major contributors in the whole C cycle (decomposition, transformation, and stabilization). Therefore, imbalances in the C cycle might be causing changes in the entire carbon content of the ecosystem. The significance of microbes, especially soil bacteria in the terrestrial carbon cycle requires more attention. This review focuses on the factors that affect microorganism behavior during the breakdown of organic materials. The key factors affecting the microbial degradation processes are the quality of the input material, nitrogen, temperature, and moisture content. In this review, we suggest that to address global climate change and its effects on agricultural systems and vice versa, there is a need to double-up on efforts and conduct new research studies to further evaluate the potential of microbial communities to reduce their contribution to terrestrial carbon emission.

Fungal community characteristics and driving factors in Bothriochloa ischaemum litter in a copper mining area

Among influencing biotic and abiotic factors, microorganisms predominate litter decomposition, playing an important role in maintaining the ecosystem material cycle. Bothriochloa ischaemum was the dominant plant species in China's Eighteen River tailings dam, and it was selected as the research object. We explored the dynamic of fungal community characteristics in B. ischaemum litter during different decomposition stages and investigated relevant driving factors affecting associative dynamic changes. Results showed that Ascomycetes and Basidiomycetes were the dominant phyla during litter decomposition. At a class level, the relative abundance of Dothideomycetes gradually decreased as litter decomposition progressed while Sordariomycetes gradually increased, ultimately becoming the dominant class. The community structure of the fungal community was mainly affected by litter pH, total carbon (TC), and copper (Cu) content. The fungal community's network structure was the most complex compared to other decomposition stages after 200 days of litter decomposition. Additionally, the fungal community's modularity gradually increased, while the degree of functional differentiation also increased, strengthening fungal community stability during litter decomposition. This study clarifies fungal community structure during litter decomposition in this copper tailings area, and provides a scientific basis for further improving soil fertility and nutrient cycling in mining areas.

Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests

Human activities are increasing the input of atmospheric particulate pollutants to forests. The components of particulate pollutants include inorganic anions, base cations and hydrocarbons. Continuous input of particulate pollutants may affect soil functioning in forests, but their effects may be modified by soil fauna. However, studies investigating how soil fauna affects the effects of particulate pollutants on soil functioning are lacking. Here, we investigated how earthworms and the particulate components interact in affecting soil enzymatic functions in a deciduous (Quercus variabilis) and a coniferous (Pinus massoniana) forest in southeast China. We manipulated the addition of nitrogen (N, ammonium nitrate), sodium (Na, sodium chloride) and polycyclic aromatic hydrocarbons (PAHs, five mixed PAHs) in field mesocosms with and without Eisenia fetida, an earthworm species colonizing forests in eastern China. After one year, N and Na addition increased, whereas PAHs decreased soil enzymatic functions, based on average Z scores of extracellular enzyme activities. Earthworms generally stabilized soil enzymatic functions via neutralizing the effects of N, Na and PAHs addition in the deciduous but not in the coniferous forest. Specifically, earthworms neutralized the effects of N and Na addition on soil pH and the effects of the addition of PAHs on soil microbial biomass. Further, both particulate components and earthworms changed the correlations among soil enzymatic and other ecosystem functions in the deciduous forest, but the effects depended on the type of particulate components. Generally, the effects of particulate components and earthworms on soil enzymatic functions were weaker in the coniferous than the deciduous forest. Overall, the results indicate that earthworms stabilize soil enzymatic functions in the deciduous but not the coniferous forest irrespective of the type of particulate components. This suggests that earthworms may neutralize the influence of atmospheric particulate pollutants on ecosystem functions, but the neutralization may be restricted to deciduous forests.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for control of natural and engineered systems. Discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28 d microcosm incubations to examine microbial community compositional and functional stability during plant-litter decomposition. Using DOC abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a "low DOC" phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as 1 solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. Importance Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

IMPORTANCE

Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition

The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.

Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns

Mat-forming fungi are common in forest and grassland soils across the world, where their activity contributes to important soil ecological processes. These fungi maintain dominance through aggressive and abundant hyphae that modify their internal physical and chemical environments and through these modifications select for what appears to be a suite of mycophilic bacteria. Here, the bacteria associated with the fungal mats of Leucopaxillus gentianeus and Leucopaxillus albissimus from western North America are compared to adjacent nonmat substrates. Within the mats, the bacterial richness and diversity were significantly reduced, and the community composition was significantly different. The bacterial community structure between the two fungal hosts was marginally significant and indicated a shared set of bacterial associates. The genera Burkholderia, Streptomyces, Bacillus, Paenibacillus, and Mycobacterium were significantly abundant within the fungal mats and represent core members of these hypha-rich environments. Comparison with the literature from fungal mat studies worldwide showed that these genera are common and often significantly found within fungal mats, further reinforcing the concept of a mycophilic bacterial guild. These genera are incorporated into a synthesis discussion in the context of our current understanding of the nature of fungal-bacterial interactions and the potential outcomes of these interactions in soil nutrient cycling, plant productivity, and human health. IMPORTANCE Fungi and bacteria are the most abundant and diverse organisms in soils (perhaps more so than any other habitat on earth), and together these microorganisms contribute to broad soil ecosystem processes. There is a suite of bacteria that appears consistently within the physical space called the hyphosphere, the area of influence surrounding fungal hyphae. How these bacteria are selected for, how they are maintained, and what broader ecological functions they perform are subjects of interest in this relatively new field-the cross-kingdom interactions between fungi and bacteria. Understanding their cooccurrence and their interactions can open new realms of understanding in soil ecological processes with global consequences.

Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting

Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and decomposing fine roots of trees become a hotspot for fungal decomposition, the fate of the bacterial component of the soil microbiome following clearcutting is unclear. Here, we investigated the response of bacterial community composition for 2 years following clearcutting of a Picea abies stand in soil, rhizosphere and tree roots, by 16S rRNA amplicon sequencing. While in the first few months after clearcutting there was no significant response of bacterial community composition in the rhizosphere and soil, bacterial communities associated with tree roots underwent more profound changes over time. Acidobacteria were abundant in rhizosphere and soil, while Firmicutes were strongly represented in the roots. In addition, bacterial communities on decomposing roots were significantly different from those on pre-clearcut live roots. Compared with fungi, the response of bacterial communities to clearcutting was much less pronounced, indicating independent development of the two microbial domains.

The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates

Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.

Enzyme kinetics inform about mechanistic changes in tea litter decomposition across gradients in land-use intensity in Central German grasslands

Grassland ecosystems provide important ecosystem services such as nutrient cycling and primary production that are affected by land-use intensity. To assess the effects of land-use intensity, operational and sensitive ecological indicators that integrate effects of grassland management on ecosystem processes such as organic matter turnover are needed. Here, we investigated the suitability of measuring the mass loss of standardized tea litter together with extracellular enzyme kinetics as a proxy of litter decomposition in the topsoil of grasslands along a well-defined land-use intensity gradient (fertilization, mowing, grazing) in Central Germany. Tea bags containing either green tea (high-quality litter) or rooibos tea (low-quality litter) were buried in 5 cm soil depth. Litter mass loss was measured after three (early-stage decomposition) and 12 months (mid-stage decomposition). Based on the fluorescence measurement of the reaction product 4-methylumbelliferone, Michaelis-Menten enzyme kinetics (V_max: potential maximum rate of activity; K_m: substrate affinity) of five hydrolases involved in the carbon (C)-, nitrogen (N)- and phosphorus (P)-cycle (β-glucosidase (BG), cellobiohydrolase (CBH), cellotriohydrolase (CTH), 1,4-β-N-acetylglucosaminidase (NAG), and phosphatase (PH)) were determined in tea litter bags and in the surrounding soil. The land-use intensity index (LUI), summarizing fertilization, mowing, grazing, and in particular the frequency of mowing were identified as important drivers of early-stage tea litter decomposition. Mid-stage decomposition was influenced by grazing intensity. The higher the potential activity of all measured C-, N- and P-targeting enzymes, the higher was the decomposition of both tea litters in the early-phase. During mid-stage decomposition, individual enzyme parameters (V_max of CTH and PH, K_m of CBH) became more important. The tea bag method proved to be a suitable indicator which allows an easy and cost-effective assessment of land-use intensity effects on decay processes in manged grasslands. In combination with enzyme kinetics it is an appealing approach to identify mechanisms driving litter break down.

Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice

Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.

Bacterial Metabolic Potential in Response to Climate Warming Alters the Decomposition Process of Aquatic Plant Litter—In Shallow Lake Mesocosms

Increased decomposition rates in shallow lakes with global warming might increase the release of atmospheric greenhouse gases, thereby producing positive feedback for global warming. However, how climate warming affects litter decomposition is still unclear in lake ecosystems. Here, we tested the effects of constant and variable warming on the bacterial metabolic potential of typically submerged macrophyte (Potamogeton crispus L.) litters during decomposition in 18 mesocosms (2500 L each). The results showed that warming reduced main chemoheterotrophic metabolic potential but promoted methylotrophy metabolism, which means that further warming may alter methane-cycling microbial metabolism. The nitrate reduction function was inhibited under warming treatments, and nitrogen fixation capability significantly increased under variable warming in summer. The changes in dissolved oxygen (DO), pH, conductivity and ammonium nitrogen driven by warming are the main environmental factors affecting the bacteria’s metabolic potential. The effects of warming and environmental factors on fermentation, nitrate reduction and ammonification capabilities in stem and leaf litter were different, and the bacterial potential in the stem litter were more strongly responsive to environmental factors. These findings suggest that warming may considerably alter bacterial metabolic potential in macrophyte litter, contributing to long-term positive feedback between the C and N cycle and climate.

Tillage Practices and Residue Management Manipulate Soil Bacterial and Fungal Communities and Networks in Maize Agroecosystems

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly impacted in 2018. Soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on soil microbial co-occurrence networks, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community and simplified soil bacterial and fungal networks in 2018. This study highlights the dissimilar responses of bacterial and fungal networks to tillage practices and emphasizes that tillage practice is more important than residue management in shaping soil microbial communities.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and ¹⁵N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N₂ fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and ¹⁵N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Bacterial community succession and influencing factors for Imperata cylindrica litter decomposition in a copper tailings area of China

Litter decomposition is a critical component of the ecological nutritional transformation process. In a copper mining area, the litter from Imperata cylindrica is the major indicator for restoring heavy metal-polluted copper mining lands. Large amounts of litter are generated at the end of the plant growing season during the process of vegetation restoration in copper mining areas, and the microbial dynamics play an important role in soil nutrient turnover during the decomposition of litter. Investigating the characteristics and interactions of bacterial communities during litter decomposition will clarify the driving mechanisms of organic matter and nutrient cycling in copper mining areas that harbor contaminated soils. Here, we report the results of an in situ decomposition experiment that lasted for a total of 460 days from three of the 16 copper mining subdams with heavy metal pollution and different phytoremediation histories (e.g., 50, 22 and 5 years) to explore the bacterial communities as the driving factors of litter decomposition. The total carbon contents of the litter decreased by 62.6% and 71.5% in the decomposition process at those sites with phytoremediation histories of 50 and 22 years (S516 and S536), respectively, but decreased by only 25.8% at the site with a phytoremediation history of 5 years (S560). The optimal C/N ratios in the three different restoration stages varied and were 65.5, 86.7 and 39.3 in S516, S536, S560, respectively. Litter decomposition enriched the heavy metal contents such as cadmium, copper (Cu), lead and zinc (P < 0.05) in litter. Proteobacteria and Actinobacteriota were the dominant bacterial phyla during the different litter decomposition stages, which accounted for 91.66% of the relative abundances in the bacterial communities. Moreover, the role of Friedmanniella, which had the highest betweenness centrality (BC) value, was critical in sustaining both the structure and function of the bacterial communities during the early decomposition stage. However, Quadrisphaera, with the maximum BC value (1074.8), became the dominant genus as litter decomposition progressed. The most crucial factors that affected the litter bacterial communities were the litter pH and copper contents. The obtained results will be helpful to provide a further understanding of litter decomposition mechanisms and will provide a scientific basis for improving the effectiveness of material circulation and nutrient transformation in degraded copper mining ecosystems.

Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.

Mesocosm Experiments Reveal Global Warming Accelerates Macrophytes Litter Decomposition and Alters Decomposition-Related Bacteria Community Structure

Global climate change scenarios predict that lake water temperatures will increase up to 4 °C and extreme weather events, such as heat waves and large temperature fluctuations, will occur more frequently. Such changes may result in the increase of aquatic litter decomposition and on shifts in diversity and structure of bacteria communities in this period. We designed a two-month mesocosm experiment to explore how constant (+4 °C than ambient temperature) and variable (randomly +0~8 °C than ambient temperature) warming treatment will affect the submerged macrophyte litter decomposition process. Our data suggests that warming treatments may accelerate the decomposition of submerged macrophyte litter in shallow lake ecosystems, and increase the diversity of decomposition-related bacteria with community composition changed the relative abundance of Proteobacteria, especially members of Alphaproteobacteria increased while that of Firmicutes (mainly Bacillus) decreased.

Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties

Although lignocellulose is the most abundant and renewable natural resource for biofuel production, its use remains under exploration because of its highly recalcitrant structure. Its deconstruction into sugar monomers is mainly driven by carbohydrate-active enzymes (CAZymes). To develop highly efficient and fast strategies to discover biomass-degrading enzymes for biorefinery applications, an enrichment process combined with integrative omics approaches was used to identify new CAZymes. The lignocellulolytic-enriched mangrove microbial community (LignoManG) established on sugarcane bagasse (SB) was enriched with lignocellulolytic bacteria and fungi such as Proteobacteria, Bacteroidetes, Basidiomycota, and Ascomycota. These microbial communities were able to degrade up to 55 % of the total SB, indicating the production of lignocellulolytic enzymes. Metagenomic analysis revealed that the LignoManG harbors 18.042 CAZyme sequences such as of cellulases, hemicellulases, carbohydrate esterases, and lytic polysaccharide monooxygenase. Similarly, our metaproteomic analysis depicted several enzymes from distinct families of different CAZy families. Based on the LignoManG data, a xylanase (coldXynZ) was selected, amplified, cloned, expressed, and biochemically characterized. The enzyme displayed psicrofilic properties, with the highest activity at 15 °C, retaining 77 % of its activity when incubated at 0 °C. Moreover, molecular modeling in silico indicated that coldXynZ is composed of a TIM barrel, which is a typical folding found in the GH10 family, and displayed similar structural features related to cold-adapted enzymes. Collectively, the data generated in this study represent a valuable resource for lignocellulolytic enzymes with potential biotechnological applications.

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas

Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.

Effects of norfloxacin on decomposition and nutrient release in leaves of the submerged macrophyte Vallisneria natans (Lour.) Hara

It is well known that antibiotic residuals affect the composition and structure of microbial communities. However, the consequences of these biological changes in terms of ecosystem function remain poorly understood, particularly in aquatic ecosystems. Here, we investigated the impacts of norfloxacin (NOR, 0, 0.5, and 8 mg L^-1), a widely used antibiotic, on the microbial community structure on leaf surfaces of the submerged macrophyte Vallisneria natans, and the corresponding variations in litter decomposition, litter nutrient release, and water properties. Results showed that after 40 days of exposure, bacterial richness consistently decreased with increasing NOR concentration, and that richness of fungi was significantly lower in treatments adding NOR than in the control treatment. Moreover, NOR shifted the community toward NOR resistant phyla and genera, especially in the bacteria community. These community shifts resulted in the inhibition of litter decomposition and nutrient release from leaf litter to system water, accompanied by increases in dissolved oxygen concentration and pH of system water. Our results indicate that, by affecting microbial communities, NOR had significant effects on litter decomposition, litter nutrient release, and water properties, highlighting the potential harmful effects of NOR on aquatic ecosystem function.

C-STABILITY an innovative modeling framework to leverage the continuous representation of organic matter

The understanding of soil organic matter (SOM) dynamics has considerably advanced in recent years. It was previously assumed that most SOM consisted of recalcitrant compounds, whereas the emerging view considers SOM as a range of polymers continuously processed into smaller molecules by decomposer enzymes. Mainstreaming this new paradigm in current models is challenging because of their ill-adapted framework. We propose the C-STABILITY model to resolve this issue. Its innovative framework combines compartmental and continuous modeling approaches to accurately reproduce SOM cycling processes. C-STABILITY emphasizes the influence of substrate accessibility on SOM turnover and makes enzymatic and microbial biotransformations of substrate explicit. Theoretical simulations provide new insights on how depolymerization and decomposers ecology impact organic matter chemistry and amount during decomposition and at steady state. The flexible mathematical structure of C-STABILITY offers a promising foundation for exploring new mechanistic hypotheses and supporting the design of future experiments.

Comparative Analyses of Phyllosphere Bacterial Communities and Metabolomes in Newly Developed Needles of Cunninghamia lanceolata (Lamb.) Hook. at Four Stages of Stand Growth

Host-plant-associated bacteria affect the growth, vigor, and nutrient availability of the host plant. However, phyllosphere bacteria have received less research attention and their functions remain elusive, especially in forest ecosystems. In this study, we collected newly developed needles from sapling (age 5 years), juvenile (15 years), mature (25 years), and overmature (35 years) stands of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook]. We analyzed changes in phyllosphere bacterial communities, their functional genes, and metabolic activity among different stand ages. The results showed that phyllosphere bacterial communities changed, both in relative abundance and in composition, with an increase in stand age. Community abundance predominantly changed in the orders Campylobacterales, Pseudonocardiales, Deinococcales, Gemmatimonadales, Betaproteobacteriales, Chthoniobacterales, and Propionibacteriales. Functional predictions indicated the genes of microbial communities for carbon metabolism, nitrogen metabolism, antibiotic biosynthesis, flavonoids biosynthesis, and steroid hormone biosynthesis varied; some bacteria were strongly correlated with some metabolites. A total of 112 differential metabolites, including lipids, benzenoids, and flavonoids, were identified. Trigonelline, proline, leucine, and phenylalanine concentrations increased with stand age. Flavonoids concentrations were higher in sapling stands than in other stands, but the transcript levels of genes associated with flavonoids biosynthesis in the newly developed needles of saplings were lower than those of other stands. The nutritional requirements and competition between individual trees at different growth stages shaped the phyllosphere bacterial community and host-bacteria interaction. Gene expression related to the secondary metabolism of shikimate, mevalonate, terpenoids, tocopherol, phenylpropanoids, phenols, alkaloids, carotenoids, betains, wax, and flavonoids pathways were clearly different in Chinese fir at different ages. This study provides an overview of phyllosphere bacteria, metabolism, and transcriptome in Chinese fir of different stand ages and highlights the value of an integrated approach to understand the molecular mechanisms associated with biosynthesis.

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.

Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

Differences in substrate use linked to divergent carbon flow during litter decomposition

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

Native Bamboo Invasions into Subtropical Forests Alter Microbial Communities in Litter and Soil

Both exotic and native plant invasions can have profound impacts on ecosystems. While many studies have examined the effects of exotic plant invasions on soil properties, relatively few have tested the effects of native plant invasions on soil microbial communities. Furthermore, we know little about the effects of native plant invasions on microbial communities in litter. In subtropical forests in southern China, we sampled litter at three decomposition stages and top soil in three forest sands representing three stages of the invasion (not invaded, moderately and heavily invaded) by the Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), a native species in China. We measured chemical properties (concentrations of C, N, P, Mg, Al, K, Ca, Mn, Cu, and Zn, and concentrations of cellulose and lignin) and microbial communities in litter and/or soil. The bamboo invasion, in general, decreased the element concentrations in litter and soil and also decreased total microbial abundance and diversity. Considering bacteria and fungi separately, the bamboo invasion decreased fungal diversity in litter and soil, but had little impact on bacterial diversity, suggesting that fungi are more sensitive and vulnerable to the bamboo invasion than bacteria. We conclude that native Moso bamboo invasions into subtropical forests may lead to a complex biogeochemical process in the litter–soil system, which may threaten local forest ecosystems by affecting microbial communities and, thus, litter decomposition and nutrient cycling.

Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility

The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.

Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes

Like larger organisms, bacteria possess traits, or phenotypic characteristics, that influence growth and impact ecosystem processes. Still, it remains unclear how these traits are organized across bacterial lineages. Using 49 bacterial strains isolated from leaf litter in Southern California, we tested the hypothesis that bacterial growth rates trade off against extracellular enzyme investment. We also tested for phylogenetic conservation of these traits under high and low resource conditions represented, respectively, by Luria broth (LB) and a monomer-dominated medium extracted from plant litter. In support of our hypotheses, we found a negative correlation between the maximum growth rate and the total activity of carbon-, nitrogen-, and phosphorus-degrading extracellular enzymes. However, this tradeoff was only observed under high resource conditions. We also found significant phylogenetic signal in maximum growth rate and extracellular enzyme investment under high and low resource conditions. Driven by our bacterial trait data, we proposed three potential life history strategies. Resource acquisition strategists invest heavily in extracellular enzyme production. Growth strategists invest in high growth rates. Bacteria in a third category showed lower potential for enzyme production and growth, so we tentatively classified them as maintenance strategists that may perform better under conditions we did not measure. These strategies were related to bacterial phylogeny, with most growth strategists belonging to the phylum Proteobacteria and most maintenance and resource acquisition strategists belonging to the phylum Actinobacteria. By accounting for extracellular enzyme investment, our proposed life history strategies complement existing frameworks, such as the copiotroph-oligotroph continuum and Grime’s competitor-stress tolerator-ruderal triangle. Our results have biogeochemical implications because allocation to extracellular enzymes versus growth or stress tolerance can determine the fate and form of organic matter cycling through surface soil.

Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates

Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.

Inconsistent response of soil bacterial and fungal communities in aggregates to litter decomposition during short-term incubation

Background

Soil aggregate-size classes and microbial communities within the aggregates are important factors regulating the soil organic carbon (SOC) turnover. However, the response of soil bacterial and fungal communities in aggregates to litter decomposition in different aggregate-size classes is poorly understand.

Methods

Soil samples from un-grazed natural grassland were separated into four dry aggregate classes of different sizes (2-4 mm, 1-2 mm, 0.25-1 mm and <0.25 mm). Two types of plant litter (leaf and stem) of Leymus chinensis were added to each of the four aggregate class samples. The CO₂ release rate, SOC storage and soil microbial communities were measured at the end of the 56-day incubation.

Results

The results showed that the 1-2 mm aggregate had the highest bacterial Shannon and CO₂ release in CK and leaf addition treatments, and the SOC in the <0.25 mm aggregate was higher than that in the others across the treatments. The relative abundance of Ascomycota was higher in the 2-4 mm and <0.25 mm aggregates than in the 1-2 mm and 0.25-1 mm aggregates in the treatment without litter addition, and the relative abundance of Aphelidiomycota was lower in the 2-4 mm and <0.25 mm aggregates than in the 1-2 mm and 0.25-1 mm aggregates. Also, litter addition increased the relative abundance of Proteobacteria and Bacteroidetes, but decreased the relative abundance of Acidobacteria, Gemmatimonadetes, and Actinobacteria. The relative abundance of Ascomycota and Aphelidiomycota increased by more than 10% following leaf litter addition. The bacterial Shannon index had a significantly positive and direct effect on SOC concentration and CO₂ release, while the fungal Shannon index was significantly correlated with SOC concentration. Our results indicate that the soil bacterial diversity contributes positively to both carbon emissions and carbon storage, whereas soil fungal diversity can promote carbon storage and decrease carbon emissions.

Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms

The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. These results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study of community function.

Microbial succession on decomposing root litter in a drought-prone Scots pine forest

Decomposition is a major flux of the carbon cycle in forest soils and understanding the involved processes is a key for budgeting carbon turnover. Decomposition is constrained by the presence of biological agents such as microorganisms and the underlying environmental conditions such as water availability. A metabarcoding approach of ribosomal markers was chosen to study the succession of bacterial and fungal decomposers on root litter. Litterbags containing pine roots were buried in a pine forest for two years and sequentially sampled. Decomposition and the associated communities were surveyed under ambient dry and long-term irrigation conditions. Early decomposition stages were characterized by the presence of fast-cycling microorganisms such as Bacteroidetes and Helotiales, which were then replaced by more specialized bacteria and litter-associated or parasitic groups such as Acidobacteria, white rots, and Pleosporales. This succession was likely driven by a decrease of easily degradable carbohydrates and a relative increase in persistent compounds such as lignin. We hypothesize that functional redundancy among the resident microbial taxa caused similar root decomposition rates in control and irrigated forest soils. These findings have important implications for drought-prone Alpine forests as frequent drought events reduce litter fall, but not litter decomposition, potentially resulting in lower carbon stocks.

Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests

Litter decomposition is the main source of mineral nitrogen (N) in terrestrial ecosystem and a key step in carbon (C) cycle. Microbial community is the main decomposer, and its specialization on specific litter is considered at the basis of higher decomposition rate in its natural environment than in other forests. However, there are contrasting evidences on how the microbial community responds to a new litter input and if the mass loss is higher in natural environment. We selected leaf litter from three different plant species across three sites of different altitudinal ranges: oak (Quercus petraea (Matt.) Liebl., 530 m a.s.l), beech (Fagus sylvatica L., 1000 m a.s.l.), rhododendron (Rhododendron ferrugineum L., 1530 m a.s.l.). A complete transplantation experiment was set up within the native site and the other two altitudinal sites. Microbial community structure was analyzed via amplified ribosomal intergenic spacer analysis (ARISA) fingerprinting. Functionality was investigated by potential enzyme activities. Chemical composition of litter was recorded. Mass loss showed no faster decomposition rate on native site. Similarly, no influence of site was found on microbial structure, while there was a strong temporal variation. Potential enzymatic activities were not affected by the same temporal pattern with a general increase of activities during autumn. Our results suggested that no specialization in microbial community is present due to the lack of influence of the site in structure and in the mass loss dynamics. Finally, different temporal patterns in microbial community and potential enzymatic activities suggest the presence of functional redundancy within decomposers.

Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances

Background

Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data.

Methods

Leaves of three species of mangrove trees typically found in the southeast of Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were collected in separate litter bags and left on three different mangroves for 60 days. These leaves were subsequently used for metagenome sequencing using Ion Torrent technology. Sequences were annotated in MG-RAST and used for network construction using MENAp.

Results

The most common phyla were Proteobacteria (classes Gamma and Alphaproteobacteria) followed by Firmicutes (Clostridia and Bacilli). The most abundant protein clusters were associated with the metabolism of carbohydrates, amino acids, and proteins. Non-metric multidimensional scaling of the metagenomic data indicated that substrate (i.e., tree species) did not significantly select for a specific community. Both networks exhibited scale-free characteristics and small world structure due to the low mean shortest path length and high average clustering coefficient. These networks also had a low number of hub nodes most of which were module hubs.

Discussion

This study demonstrates that under different environmental pressures (i.e., plant species or mangrove location) the microbial community associated with the decaying material forms a robust and stable network.