Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests

Soil Organic Carbon Chemical Functional Groups under Different Revegetation Types Are Coupled with Changes in the Microbial Community Composition and the Functional Genes

Different revegetatiom types can affect the chemical composition of soil organic carbon (SOC), soil microbial community and the functional genes related to carbon cycle. However, the relationships between SOC chemical functional groups and soil microbial communities and the functional genes remains poorly unclear under different revegetation types. Using the solid-state 13C nuclear magnetic resonance (NMR) spectroscopy, we examined changes in the SOC chemical composition of five soils (0–10 cm depth) from Larix gmelinii Rupr. (LG), Pinus koraiensis Sieb. (PK), Quercus mongolica Fisch. (QM), Juglans mandshurica Maxim. (JM), and conifer-broadleaf forest (CB). And the soil microbial community genes related to metabolism of macro-molecular compounds were determined via whole genome shotgun based on Illumina HiSeq. Our results indicated that broadleaf forests (JM, QM) had increased the contents of soil total carbon (C), total nitrogen (N), dissolved organic carbon (DOC), and microbial biomass carbon (MBC), compared with coniferous forests (LG, PK) and the conifer-broadleaf forest (CB). While, the coniferous forests generated a lower O-alcoxyl C, a higher alkyl C, and the ratio of alkyl C/O-alkyl C than broadleaf forests. A total of four kingdoms were identified via whole metagenome shotgun sequencing, including eight archaea, 55 bacteria, 15 eukaryota, and two viruses, giving a total 80 phyla. The contents of alkyne C, phenolic C, methoxyl C, COO/NC=O, and alkyl C were strong related to the composition of soil microbial community and their contents illuminated a major part of the variation in soil microbial composition. We detected seven corresponding macro-molecular compounds of different organic carbon functional group, and 244 genes related to metabolism across all samples, and soil total C, total N, and DOC could be the main factors for microbial functional gene composition. Interestingly, the relative abundances of different SOC chemical functional groups, the phylogenetic distance for microbes, the genes of C cycling based on the KEGG database, and the relative abundance of genes related to metabolism of macro-molecular compounds of different SOC chemical functional groups under different revegetation types all could be divided into three groups, including PK plus LG, JM plus QM, and CB. Our results also illustrated that variations in SOC chemical functional groups were strongly associated with changes of soil microbial community taxa and functional genes, which might be affected by the changes of soil characteristics.

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N₂ fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.

Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N₂ fixation is the major source of biologically available N, the soil N₂-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.

Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes

Seedling emergence is a critical stage in the establishment of desert plants. Soil microbes participate in plant growth and development, but information is lacking with regard to the role of microbes on seedling emergence. We applied the biocides (captan and streptomycin) to assess how seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence of Artemisia sphaerocephala on the desert sand dune. Fungal and bacterial community composition and diversity and fungal-bacterial interactions were changed by both captan and streptomycin. Mucilage increased soil enzyme activities and fungal-bacterial interactions. Highest seedling emergence occurred under streptomycin and mucilage treatment. Members of the phyla Firmicutes and Glomeromycota were the keystone species that improved A. sphaerocephala seedling emergence, by increasing resistance of young seedlings to drought and pathogen. Seed mucilage directly improved seedling emergence and indirectly interacted with the soil microbial community through strengthening fungal-bacterial interactions and providing favourable environment for soil enzymes to affect seedling emergence. Our study provides a comprehensive understanding of the regulatory mechanisms by which soil microbial community and seed mucilage interactively promote successful establishment of populations of desert plants on the barren and stressful sand dune.

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems.

Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability

Eutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%-12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon-degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4-17 folds and recalcitrant carbon-degrading genes by 23%-40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space

BACKGROUND

Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells.

RESULTS

Equipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P < 0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed phage-prokaryote pairs were shallowly conserved since they were detected only within small viral clades.

CONCLUSIONS

Those results collectively demonstrate phages as a major biotic factor in controlling prokaryotic composition and process performance. Therefore, phages may play a larger role in shaping prokaryotic community dynamics and process performance of anaerobic digesters than currently appreciated.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation

The study of soil microbial responses to environmental changes is useful to improve simulation models and mitigation strategies for climate change. We here investigated two Alpine forest sites (deciduous forest vs. coniferous forest) situated at different altitudes (altitudinal effect) in spring and autumn (seasonal effect) regarding: (i) bacterial and fungal abundances (qPCR); (ii) diversity and structure of bacterial and fungal communities (amplicon sequencing); and (iii) diversity and composition of microbial functional gene community (Geochip 5.0). Significant altitudinal changes were detected in microbial abundances as well as in diversity and composition of taxonomic and functional communities as a consequence of the differences in pH, soil organic matter (SOM) and nutrient contents and soil temperatures measured between both sites. A network analysis revealed that deciduous forest site (at lower altitude) presented a lower resistance to environmental changes than that of coniferous forest site (at higher altitude). Significant seasonal effects were detected only for the diversity (higher values in autumn) and composition of microbial functional gene community, which was related to the non-significant increased SOM and nutrient contents detected in autumn respect to spring and the presumable high capacity of soil microbial communities to respond in functional terms to discreet environmental changes.

Variations of Soil Microbial Community Structures Beneath Broadleaved Forest Trees in Temperate and Subtropical Climate Zones

Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRI (Net Relatedness Index) values increased from -0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomy-based association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-for-time substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.

Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota

Recently, several investigations focused on the discovery of a bacterial consortium shared among different wastewater treatment plants (WWTPs). Nevertheless, the definition of a core microbiota over time represents the necessary counterpart in order to unravel the dynamics of bacterial communities in these environments. Here we performed a monthly survey on the bacterial community of a consortial industrial plant. Objectives of this study were: (1) to identify a core microbiota constant over time; (2) to evaluate the temporal dynamics of the community during one year. A conspicuous and diversified core microbiota is constituted by operational taxonomic units which are present throughout the year in the plant. Community composition data confirm that the presence and abundance of bacteria in WWTPs is highly consistent at high taxonomic level. Our results indicate however a difference in microbial community structure between two groups of samples, identifying the summer holiday period as the break-point. Changes in the structure of the microbial community occur otherwise gradually, one month after another. Further studies will clarify how the size and diversity of the core microbiota could affect the observed dynamics.

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO₂ efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available.