Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem

Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m-2 y-1). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m-2 y-1) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4+-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4+-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.

Regulation of wheat growth by soil multifunctionality and metagenomic-based microbial functional profiles under mulching treatments

Soil microbial functional genes play key roles in biogeochemical processes that are closely related to crop development. However, the regulation of crop growth by the composition and potential interactions of metagenomic-based functional genes is poorly understood. Therefore, in a long-term mulching experiment, the regulation of wheat growth by soil multifunctionality, microbial functional profiles driven by soil properties and microbial activity was studied. Soil properties and microbial activity were significantly separated into distinct mulching treatments, and were significantly declined by plastic film mulching treatment, similar to soil multifunctionality. Only carbon (C) and phosphorus (P) cycling gene compositions were divided significantly into distinct mulching treatments to varying degrees. Similarly, intra- and inter-connected sub-networks associated with C and P cycling genes were more complex and stable than the sub-networks containing nitrogen cycling genes. Despite core functional genes being located in the middle of each network, they were rarely observed in the metagenomic assembly genomes. Subsequently, the dominant soil properties and microbial activity had greater effects on C cycling gene composition and network, which played essential roles in wheat growth regulation. Overall, wheat yield and biomass were affected differently by straw and plastic film mulching treatments, and were mainly regulated by C cycling gene network and soil multifunctionality, respectively. The results of the present study provide novel insights into wheat growth regulation by soil microbial functional profiles, with potential implications for sustainable crop production in mulching conservation agroecosystems.

Molecular insights into the microbial degradation of sediment-derived DOM in a macrophyte-dominated lake under aerobic and hypoxic conditions

The mineralization of dissolved organic matter (DOM) in sediments is an important factor leading to the eutrophication of macrophyte-dominated lakes. However, the changes in the molecular characteristics of sediment-derived DOM during microbial degradation in macrophyte-dominated lakes are not well understood. In this study, the microbial degradation process of sediment-derived DOM in Lake Caohai under aerobic and hypoxic conditions was investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics. The results revealed that the microbial degradation of sediment-derived DOM in macrophyte-dominated lakes was more intense under aerobic conditions. The microorganisms mainly metabolized the protein-like substances in the macrophyte-dominated lakes, and the carbohydrate-active enzyme genes and protein/lipid-like degradation genes played key roles in sediment-derived DOM degradation. Organic compounds with high H/C ratios such as lipids, carbohydrates, and protein/lipid-like compounds were preferentially removed by microorganisms during microbial degradation. Meanwhile, there was an increase in the abundance of organic molecular formula with a high aromaticity such as tannins and unsaturated hydrocarbons with low molecular weight and low double bond equivalent. In addition, aerobic/hypoxic environments can alter microbial metabolic pathways of sediment-derived DOM by affecting the relative abundance of microbial communities (e.g., Gemmatimonadetes and Acidobacteria) and functional genes (e.g., ABC.PE.P1 and ABC.PE.P) in macrophyte-dominated lakes. The abundances of lipids, unsaturated hydrocarbons, and protein compounds in aerobic environments decreased by 58 %, 50 %, and 44 %, respectively, compared to in hypoxic environments under microbial degradation. The results of this study deepen our understanding of DOM biodegradation in macrophyte-dominated lakes under different redox environments and provide new insights into nutrients releases from sediment and continuing eutrophication in macrophyte-dominated lakes.

Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China

Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p > 0.05) and the amylase gene abundance decreased firstly in middle-succession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Inhibition of Spartina alterniflora growth alters soil bacteria and their regulation of carbon metabolism

The state of growth of invasive species has a significant impact on the microbial regulation of the soil carbon (C) cycle. This study focused on the growth of Spartina alterniflora treated with imazapyr in the Tiaozini wetland of Jiangsu Province, China. The changes in soil bacterial structure, bacterial C metabolic activity, soil C, and regulation mechanism of soil C metabolic activity by biotic and abiotic factors were investigated. The results showed that soil bacterial diversity eventually decreased significantly (p < 0.05) along with significant changes in microbial structure (p < 0.05). Significant changes in soil physicochemical properties due to S. alterniflora growth inhibition were the key factors affecting the changes in the soil bacterial taxa composition (p < 0.05). Abiotic factors showed a greater effect on metabolic activities related to C fixation and biosynthesis of bacterial taxa than biotic factors (self-regulation). Additionally, bacterial taxa regulated soil C emission and degradation to a greater extent than abiotic factors. This study provides important information for understanding the regulators of C cycling in coastal wetland soil during the control of S. alterniflora invasion by imazapyr; moreover, it provides a scientific basis for the government to establish a prevention and control policy for S. alterniflora invasion. Understanding the complex interplay between abiotic and biotic factors is essential for developing effective strategies to manage soil C and mitigate the impacts of climate change.

Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation

The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.

Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China

To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.

The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.

Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands

Atmospheric trace gases, such as H₂ and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H₂ and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.

Soil microbes support Janzen’s mountain passes hypothesis: The role of local-scale climate variability along a tropical montane gradient

Tropical montane ecosystems are the centers of biodiversity, and Janzen proposed that mountain climate variability plays a key role in sustaining this biodiversity. We test this hypothesis for soil bacteria and fungi along a 265–1,400 m elevational gradient on Hainan Island of tropical China, representing diverse vegetation types from deciduous monsoon forest to cloud forest. We found that bacterial and fungal diversity declined as elevation increased, and the dissimilarity of both groups increased with increasing separation in elevation, although changes in bacteria were larger than in fungi. Seasonal alterations and the range of soil moisture in the growing season were found to be the dominant drivers of fungal richness and Shannon diversity, whereas soil pH was the major driver of bacterial diversity. Dissimilarities of bacterial and fungal communities were best predicted by climate, particularly seasonal changes in soil temperature, with weaker influences of soil physicochemistry and vegetation. The dominant effect of seasonality in soil temperature was further detected in cloud forests, which harbored a higher proportion of unique bacterial species and dissimilarity of bacterial and fungal communities. Our findings suggest that local-climate variability plays a crucial role in structuring the distribution of soil microbial communities along a tropical montane gradient, which generally supports Janzen’s hypothesis. Such a sensitivity to climatic variability suggests that soil microbial communities along tropical montane gradients may shift in response to future climate scenarios.

Nitrogen fertilization rates mediate rhizosphere soil carbon emissions of continuous peanut monoculture by altering cellulose-specific microbess

INTRODUCTION

Crops influence both soil microbial communities and soil organic carbon (SOC) cycling through rhizosphere processes, yet their responses to nitrogen (N) fertilization have not been well investigated under continuous monoculture.

METHODS

In this study, rhizosphere soil microbial communities from a 5-year continuous mono-cropped peanut land were examined using Illumina HighSeq sequencing, with an N fertilization gradient that included 0 (N0), 60 (N60), 120 (N120) and 180 (N180) kg hm^-2. Soil respiration rate (R _s) and its temperature sensitivity (Q ₁₀) were determined, with soil carbon-acquiring enzyme activities assayed.

RESULTS AND DISCUSSION

The obtained results showed that with N fertilization, soil mineral N (N_min) was highly increased and the soil C/N ratio was decreased; yields were unchanged, but root biomass was stimulated only at N120. The activities of β-1,4-glucosidase and polyphenol oxidase were reduced across application rates, but that of β-1,4-cellobiohydrolase was increased only at N120. Bacterial alpha diversity was unchanged, but fungal richness and diversity were increased at N60 and N120. For bacterial groups, the relative abundance of Acidobacteria was reduced, while those of Alphaproteobacteria and Gammaproteobacteria were increased at N60 and N120. For fungal members, the pathogenic Sordariomycetes was inhibited, but the saprotrophic Agaricomycetes was promoted, regardless of N fertilization rates. RDA identified different factors driving the variations in bacterial (root biomass) and fungal (N_min) community composition. N fertilization increased R _s slightly at N60 and significantly at N120, mainly through the promotion of cellulose-related microbes, and decreased R _s slightly at N180, likely due to carbon limitation. N fertilization reduced microbial biomass carbon (MBC) at N60, N120 and N180, decreased SOC at N120 and N180, and suppressed dissolved organic carbon (DOC) at N180. In addition, the unchanged Q ₁₀ may be a joint result of several mechanisms that counteracted each other. These results are of critical importance for assessing the sustainability of continuously monocultured ecosystems, especially when confronting global climate change.

Metagenomics reveals N-induced changes in carbon-degrading genes and microbial communities of tea (Camellia sinensis L.) plantation soil under long-term fertilization

Soil organic carbon (SOC) is an important C pool of the global ecosystem and is affected by various agricultural practices including fertilization. Excessive nitrogen (N) application is an important field management measure in tea plantation systems. However, the mechanism underlying the impact of N fertilization on SOC, especially the microscopic mechanism remain unclear. The present study explored the effects of N fertilization on C-cycling genes, SOC-degrading enzymes and microbes expressing these enzymes by using a metagenomic approach in a tea plantation under long-term fertilization with different N rates. Results showed that N application significantly changed the abundance of C-cycling genes, SOC-degrading enzymes, especially those associated with labile and recalcitrant C degradation. In addition, the beta-glucosidase and chitinase-expressing microbial communities showed a significant difference under different N rates. At the phylum level, microbial taxa involved in C degradation were highly similar and abundant, while at the genus level, only specific taxa performed labile and recalcitrant C degradation; these SOC-degrading microbes were significantly enriched under N application. Redundancy analysis (RDA) revealed that the soil and pruned litter properties greatly influenced the SOC-degrading communities; pH and DOC of the soil and biomass and total polyphenol (TP) of the pruned litter exerted significant effects. Additionally, the random forest (RF) algorithm revealed that soil pH and dominant taxa efficiently predicted the beta-glucosidase abundance, while soil pH and DOC, pruned litter TP, and the highly abundant microbial taxa efficiently predicted chitinase abundance. Our study indicated that long-term N fertilization exerted a significant positive effect on SOC-degrading enzymes and microbes expressing these enzymes, resulting in potential impact on soil C storage in a perennial tea plantation ecosystem.

Soil bacterial community changes along elevation gradients in karst graben basin of Yunnan-Kweichow Plateau

Elevation gradients could provide natural experiments to examine geomorphological influences on biota ecology and evolution, however little is known about microbial community structures with soil depths along altitudinal gradients in karst graben basin of Yunnan-Kweichow Plateau. Here, bulk soil in A layer (0 ~ 10 cm) and B layer (10 ~ 20 cm) from two transect Mounts were analyzed by using high-throughput sequencing coupled with physicochemical analysis. It was found that the top five phyla in A layer were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia, and the top five phyla in B layer were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi in a near-neutral environment. Edaphic parameters were different in two layers along altitudinal gradients. Besides that, soil microbial community compositions varied along altitudinal gradient, and soil organic carbon (SOC) and total nitrogen (TN) increased monotonically with increasing elevation. It was further observed that Shannon indexes with increasing altitudes in two transect Mounts decreased monotonically with significant difference (p = 0.001), however beta diversity followed U-trend with significant difference (p = 0.001). The low proportions of unique operational taxonomic units (OTUs) appeared at high altitude areas which impact the widely accepted elevation Rapoport's rules. The dominant Bradyrhizobium (alphaproteobacterial OTU 1) identified at high altitudes in two layers constitutes the important group of free-living diazotrophs and could bring fixed N into soils, which simultaneously enhances SOC and TN accumulation at high altitudes (p < 0.01). Due to different responses of bacterial community to environmental changes varying with soil depths, altitudinal gradients exerted negative effects on soil bacterial communities via soil physical properties and positive effects on soil bacterial diversities via soil chemical properties in A layer, however the results in B layer were opposite. Overall, our study is the first attempt to bring a deeper understanding of soil microbial structure patterns along altitudinal gradients at karst graben basin areas.

Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.

Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism

Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.

Embracing mountain microbiome and ecosystem functions under global change

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.

Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds

The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial communities was similar between SC and SCC, but the water and sediments shared few common members in either pond. The relative abundances of N cycling genes were significantly higher in sediment than in water in both SC and SCC, except for assimilatory nitrate reduction genes. The main drivers of the differences in the relative abundances of N cycling genes in SC and SCC were salinity and pH in water and the NO2− and NH4+ contents of pore water in sediment. These results indicate that the coculture of S. constricta in a shrimp-crab pond may result in decreased N cycling in sediment. The reduced N flux in the shrimp IMTA ponds primarily originates within the sediment, except for assimilatory nitrate reduction.