High soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River

Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4+-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.

Soil pH and carbon quality index regulate the biogeochemical cycle couplings of carbon, nitrogen and phosphorus in the profiles of Isohumosols

Soil biogeochemical cycles are essential for regulating ecosystem functions and services. However, little knowledge has been revealed on microbe-driven biogeochemical processes and their coupling mechanisms in soil profiles. This study investigated the vertical distribution of soil functional composition and their contribution to carbon (C), nitrogen (N) and phosphorus (P) cycling in the humus horizons (A-horizons) and parent material horizons (C-horizons) in Udic and Ustic Isohumosols using shotgun sequencing. Results showed that the diversity and relative abundance of microbial functional genes was influenced by soil horizons and soil types. In A-horizons, the relative abundances of N mineralization and liable C decomposition genes were significantly greater, but the P cycle-related genes, recalcitrant C decomposition and denitrification genes were lower compared to C-horizons. While, Ustic Isohumosols had lower relative abundances of C decomposition genes but higher relative abundances of N mineralization and P cycling-related pathways compared to Udic Isohumosols. The network analysis revealed that C-horizons had more interactions and stronger stability of functional gene networks than in A-horizons. Importantly, our results provide new insights into the potential mechanisms for the coupling processes of soil biogeochemical cycles among C, N and P, which is mediated by specific microbial taxa. Soil pH and carbon quality index (CQI) were two sensitive indicators for regulating the relative abundances and the relationships of functional genes in biogeochemical cycles. This study contributes to a deeper understanding of the ecological functions of soil microorganisms, thus providing a theoretical basis for the exploration and utilization of soil microbial resources and the development of soil ecological control strategies.

Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora

Ageratina adenophora is an invasive weed species found in many countries. Methods to control the spread of this weed have been largely unsuccessful. Soil pH is the most important soil factor affecting the availability of nutrients for plant and impacting its growth. Understanding the mechanisms of the influence of soil pH on the growth of A. adenophora may help to develop effective control measures. In this study, we artificially changed the soil pH in pot experiments for A. adenophora. We studied the effects of acidic (pH 5.5), weakly acidic (pH 6.5), neutral (pH 7.2), and alkaline (pH 9.0) soils on the growth, availability of soil nutrients, activity of antioxidant enzymes, levels of redox markers in the leaves, and the structure and diversity of the rhizosphere microbiome. Soil with a pH 7.2 had a higher (47.8%) below-ground height versus soils of pH 5.5 at day 10; plant had a higher (11.3%) above-ground height in pH 7.2 soils than pH 9.0 soils at day 90; no differences in the fresh and dry weights of its above- and belowground parts, plant heights, and root lengths were observed in plants growing in acid, alkaline, or neutral pH soil were observed at day 180. Correspondingly, the antioxidant enzymes SOD (superoxide dismutase), POD (peroxidase), CAT (catalase) and redox markers GSH (glutathione) and MDA (malondialdehyde) were measured in the leaves. Significant differences existed in the activities of CAT and the levels of GSH between those growing in acidic and alkaline soils and those in neutral pH soil at day 90; however, only lower (36.8%) CAT activities in those grown at pH 5.5 than those grown at pH 7.2 were found at day 180. Similarly, significant differences in available P (16.89 vs 3.04 mg Kg-1) and total K (3.67 vs 0.96 mg Kg-1), total P (0.37 vs 0.25 g Kg-1) and total N (0.45 vs 1.09 g Kg-1) concentrations were found between the rhizosphere soils of A. adenophora grown at pH 9.0 and 7.2 at day 90; no such differences were seen at day 180. High throughput analyses of the 16S rRNA and ITS fragments showed that the rhizosphere microbiome diversity and composition under different soil pH conditions changed over 180 days. The rhizosphere microbiomes differed in diversity, phylum, and generic composition and population interactions under acid and alkaline conditions versus those grown in neutral soils. Soil pH had a greater impact on the diversity and composition of the prokaryotic rhizosphere communities than those of the fungal communities. A. adenophora responded successfully to pH stress by changing the diversity and composition of the rhizosphere microbiome to maintain a balanced nutrient supply to support its normal growth. The unusual pH tolerance of A. adenophora may be one crucial reason for its successful invasion. Our results suggest that attempts use soil pH to control its invasion by changing the soil pH (for example, using lime) will fail.

Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas

IMPORTANCE

The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.

Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale

Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12-month high-frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre-mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll-a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi-nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.

Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea

The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.

Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure

Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.

Impact of Insect-Resistant Transgenic Maize 2A-7 on Diversity and Dynamics of Bacterial Communities in Rhizosphere Soil

Artificial modification of Bacillus thuringiensis (Bt) proteins can effectively improve their resistance to target pests, but the effect of such modification on the diversity of rhizosphere microorganisms remains unclear. Transgenic maize 2A-7 contains two artificially modified Bt proteins, mCry1Ab and mCry2Ab. These proteins can enter soil and pose a potential threat to soil microbial diversity. To assess their impacts on rhizosphere bacteria communities, the contents of the two Bt proteins and changes in bacterial community diversity in the rhizosphere soils of transgenic maize 2A-7 and its control variety were analyzed at different growth stages in 2020. The results showed that the two Bt proteins were detected at low levels in the rhizosphere soils of 2A-7 plants. No significant differences in soil bacterial diversity were detected between 2A-7 and its control variety at any of the growth stages. Bioinformatics analysis indicated that the growth stage, rather than the cultivar, was the main factor causing changes in bacterial communities. This research provides valuable data for understanding the impact of Bt crops on the soil microbiome, and establishes a theoretical basis for evaluation of their safety.

Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships

Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.

Acidity drives volatile metabolites in the spontaneous fermentation of sesame flavor-type baijiu

Environmental factors play an important role in contributing to intricate compositional dynamics and volatile metabolites in food fermentation. However, our understanding of which and how environmental factors affect volatile metabolites during sesame flavor-type baijiu fermentation is poor. Here, we examined the effects of environmental factors on the bacterial and fungal community to determine how changes in representative factors impact the microbial structure, diversity, and volatile metabolites in three fermentations. Results showed that bacterial community (ANOSIM: R = 0.79, P = 0.001), fungal community (ANOSIM: R = 0.65, P = 0.001), and volatile metabolites (ANOSIM: R = 0.84, P = 0.001) were significantly different in three fermentations. Acidity, ethanol, and moisture negatively impacted bacterial composition and diversity (P < 0.05). The fungal diversity and structure were positively and significantly affected by acidity (path coefficient, b = 0.54 for diversity, b = 0.35 for structure, P < 0.05). The fungal community rather than the bacterial community was the strongest driver of volatile metabolites. Fungal structure and diversity were equally important for the composition and content of volatile metabolites (structure: b = 0.50, diversity: b = 0.56, P < 0.05). 66 % of variations in volatile metabolites could be explained. Altogether these results indicated that acidity strongly drove volatile metabolites by modulating fungal structure and diversity. This work provides insights into managing volatile metabolites by regulating initial acidity in sesame flavor-type baijiu fermentation.

Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice

Wild rice has been demonstrated to possess enriched genetic diversity and multiple valuable traits involved in disease/pest resistance and abiotic stress tolerance, which provides a potential resource for sustainable agriculture. However, unlike the plant compartments such as rhizosphere, the structure and assembly of phyllosphere microbial communities of wild rice remain largely unexplored. Through amplicon sequencing, this study compared the phyllosphere bacterial and fungal communities of wild rice and its neighboring cultivated rice. The core phyllosphere microbial taxa of both wild and cultivated rice are dominated with Pantoea, Methylobacterium, Nigrospora, and Papiliotrema, which are potentially beneficial to rice growth and health. Compared to the cultivated rice, Methylobacterium, Sphingomonas, Phaeosphaeria, and Khuskia were significantly enriched in the wild rice phyllosphere. The potentially nitrogen-fixing Methylobacterium is the dominated wild-enriched microbe; Sphingomonas is the hub taxon of wild rice networks. In addition, the microbiota of wild rice was more governed by deterministic assembly with a more complicated and stable community network than the cultivated rice. Our study provides a list of the beneficial microbes in the wild rice phyllosphere and reveals the microbial divergence between wild rice and cultivated rice in the original habitats, which highlights the potential selective role of wild rice in recruiting specific microbiomes for enhancing crop performance and promoting sustainable food production. IMPORTANCE Plant microbiota are being considered a lever to increase the sustainability of food production under a changing climate. In particular, the microbiomes associated with ancestors of modern cultivars have the potential to support their domesticated cultivars. However, few efforts have been devoted to studying the biodiversity and functions of microbial communities in the native habitats of ancestors of modern crop species. This study provides a list of the beneficial microbes in the wild rice phyllosphere and explores the microbial interaction patterns and the functional profiles of wild rice. This information could be useful for the future utilization of the plant microbiome to enhance crop performance and sustainability, especially in the framework of sustainable agroecosystems.

Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea

The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.

Determining the contribution of microbiome complexity to the soil nutrient heterogeneity of fertile islands in a desert ecosystem

"Fertile islands" are known as hotspots of soil nutrient spatial heterogeneity in dryland ecosystems. Although soil microorganisms play critical functional roles in nutrient capture and cycling within fertile islands, our understanding of polymicrobial community roles in regulating soil nutrient distribution in fertile islands remains limited. Herein, we aim to clarify the relationships between the complexity of soil microbial (bacterial, archaeal and fungal) communities and the nutrient distribution around fertile islands. Soil samples were collected along vertical profiles at varying depths in three patches under the canopy of Hedysarum scoparium (CENTRE), at the edge (EDGE) of the canopy and outside (OUTSIDE) the canopy in an area of flowing sand. All the three microbiota have showed spatial heterogeneity around the fertile islands. Among them, bacteria had the most significant heterogeneity, and bacterial community assembly was dominated by deterministic processes. Microbial interaction patterns also showed spatial heterogeneity among different patches. More interaction complexity within microbiota was found in the bacteria in the CENTRE patch and in the fungi in the OUTSIDE patch. In addition, the proportions of among-kingdom connections were reduced under the canopies. Bacteria had the highest connectivity and centrality in the polymicrobial networks and were the most important predictor of polymicrobial interaction complexity, which may have contributed to the distribution of soil nutrients. The random forest (RF) model provided evidence that bacterial beta-diversity and the polymicrobial network complexity index can be optimal predictors of the soil multinutrient cycling index. Our study highlighted the responses of bacteria and polymicrobial interactions to fertile islands and their importance in driving soil nutrient heterogeneity. This information will help in managing soil microorganisms to provide dryland ecosystem services.

Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau

Introduction

Fritillaria przewalskii Maxim. is a Chinese endemic species with high medicinal value distributed in the northeastern part of the Tibetan Plateau. F. przewalskii root-associated rhizosphere bacterial communities shaped by soil properties may maintain the stability of soil structure and regulate F. przewalskii growth, but the rhizosphere bacterial community structure of wild F. przewalskii from natural populations is not clear.

Methods

In the current study, soil samples from 12 sites within the natural range of wild F. przewalskii were collected to investigate the compositions of bacterial communities via high-throughput sequencing of 16S rRNA genes and multivariate statistical analysis combined with soil properties and plant phenotypic characteristics.

Results

Bacterial communities varied between rhizosphere and bulk soil, and also between sites. Co-occurrence networks were more complex in rhizosphere soil (1,169 edges) than in bulk soil (676 edges). There were differences in bacterial communities between regions, including diversity and composition. Proteobacteria (26.47-37.61%), Bacteroidetes (10.53-25.22%), and Acidobacteria (10.45-23.54%) were the dominant bacteria, and all are associated with nutrient cycling. In multivariate statistical analysis, both soil properties and plant phenotypic characteristics were significantly associated with the bacterial community (p < 0.05). Soil physicochemical properties accounted for most community differences, and pH was a key factor (p < 0.01). Interestingly, when the rhizosphere soil environment remained alkaline, the C and N contents were lowest, as was the biomass of the medicinal part bulb. This might relate to the specific distribution of genera, such as Pseudonocardia, Ohtaekwangia, Flavobacterium (relative abundance >0.01), which all have significantly correlated with the biomass of F. przewalskii (p < 0.05).

Discussion

F. przewalskii is evidently averse to alkaline soil with high potassium contents, but this requires future verification. The results of the present study may provide theoretical guidance and new insights for the cultivation and domestication of F. przewalskii.

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.

Microbial network complexity drives non-linear shift in biodiversity-nutrient cycling in a saline urban reservoir

Aquatic biodiversity is important in mediating ecosystem functioning, contributing to ecosystem sustainability and human wellbeing. However, how microbial network complexity affects the biodiversity-nutrient cycling relationship in saline freshwater ecosystems remains underexplored. Using high-resolution time-series data, we examined the relationships between microeukaryotic-bacterial community network complexity, biodiversity and multi-nutrient cycling in an urban reservoir undergoing a freshwater salinization-desalinization cycle. We found that low microbial diversity enhanced ecosystem multi-nutrient cycling under high salinity stress. In addition, multi-nutrient cycling declined with increased network complexity. Further, we found a non-linear relationship between salinity-induced shifts in the complexity of the microbial network and biodiversity-nutrient cycling (BNC) relationship of keystone taxa, i.e. the strength of the BNC relationship first became weak and then strong with increased network complexity. Together, these results highlighted the significant insight that there is not always positive relationship between biodiversity/network complexity and multi-nutrient cycling, even between network complexity and BNC relationship in real-world ecosystems, suggesting that preserving microbial association is important in aquatic health managing and evaluating the freshwater salinization problem.

Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau

Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.

Archaeal communities perform an important role in maintaining microbial stability under long term continuous cropping systems

Long-term continuous cropping of soybean can generate the development of disease-suppressive soils. However, whether the changes in microbial communities, especially for archaea, contribute to controlling soil sickness and improving crop yields remains poorly understood. Here, real-time PCR and high-throughput sequencing were employed to investigate the changes in soil archaeal communities in both bulk and rhizosphere soils under four cropping systems, including the continuous cropping of soybeans for a short-term of 3 and 5 years (CC3 and CC5, respectively) and for a long-term of 13 years (CC13), as well as a soybean-maize rotation for 5 years (CR5). The results showed that CC13 and CR5 significantly increased archaeal abundance, reduced the alpha-diversity of archaeal communities, and changed soil archaeal community structures compared to CC3 and CC5. Microbial co-occurrence network analysis revealed that CC13 led to the higher resistant microbial community and lower the relative abundance of potential plant pathogens in the network compared to CC3 and CC5. Correlation analysis showed that the microbial resistance index was negatively correlated with the relative abundance of potential plant pathogens and positively correlated with soybean yields in both bulk and rhizosphere soils. Intriguingly, the random forest (RF) analysis showed that archaea contributed the most to soil microbial resistance even though they were not at the core positions of the network. Overall, structural equation models (SEMs) revealed that high resistant microbial community could directly or indirectly improved soybean yields by regulating the relative abundance of plant pathogens and the soil nutrients, suggesting that the regulation of soil microbial taxa may play an important role in maintaining agricultural productivity under continuous cropping of soybean.

Environmental factors, bacterial interactions and plant traits jointly regulate epiphytic bacterial community composition of two alpine grassland species

Epiphytic microbes on the surfaces of leaves and roots can bring substantial benefits or damages to their plant hosts. Although various factors have been proposed for shaping the epiphytic microbial composition, the contributions of environment factors, endogenous microbial taxa interactions, host plant traits, and their interactive effects are poorly understood. Here, we conducted a field investigation along a precipitation gradient and collected leaf and root surface microbes of two alpine plant species for 16S rRNA sequencing. We found that epiphytic bacterial community composition significantly changed along the precipitation gradient through ordination analyses and permutational multivariate analysis of variance. Beneficial bacterial taxa from Caulobacteraceae, Sphingomonadaceae, Comamonadaceae and Rhizobiales were enriched in the high precipitation zones. The stress-tolerant Hymenobacteraceae, Micrococcaceae, and Geodermatophilaceae occurred more frequently in the phyllosphere, and the Thermoleophilia, Thermomicrobiales and Bacillales were enriched in the rhizosphere at the drier sites. Mean annual precipitation was the most important factor regulating the epiphytic bacterial community composition. The direct effect of climate on bacterial community composition was higher in the phyllosphere than in the rhizosphere where joint effects of climate, plant traits and soil properties predominated. Distinct leaf trichome cover and plant height clearly explained the host effect on the phyllosphere bacterial community composition while belowground traits did not explain the host effect well on the rhizosphere bacterial community composition. We detected a significant role of bacterial taxa interactions in shaping microbial communities, where greater negative taxa interactions led to lesser composition changes. Structural equation modeling showed that environmental factors and bacterial interactions substantially contributed to the variation in epiphytic community composition, followed by host plant traits. This study advances our understanding of complex factors affecting alpine epiphytic community assembly and further confirms the role of biotic interactions.

Plants Play Stronger Effects on Soil Fungal than Bacterial Communities and Co-Occurrence Network Structures in a Subtropical Tree Diversity Experiment

Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. However, the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in association with tree species richness gradients are poorly documented. Here, we examined soil fungal and bacterial communities in a Chinese subtropical tree species richness experiment (from 1 to 16 species) using amplicon sequencing targeting the internal transcribed spacer 2 and V4 hypervariable region of the rRNA genes, respectively. Tree species richness had no significant effect on the diversity of either fungi or bacteria. In addition to soil and spatial distance, tree species richness and composition had a significant effect on fungal community composition but not on bacterial community composition. In fungal rather than bacterial co-occurrence networks, the average degree, degree centralization, and clustering coefficient significantly decreased, but the modularity significantly increased with increasing tree species richness. Fungal co-occurrence network structure was influenced by tree species richness and community composition as well as the soil carbon: nitrogen ratio, but the bacterial co-occurrence network structure was affected by soil pH and spatial distance. This study demonstrates that the community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria differ in the subtropical forest. IMPORTANCE Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. Therefore, revealing the mechanisms associated with community assembly and co-occurrence network structure of microbes along plant species diversity gradients is very important for understanding biodiversity maintenance and community stability in response to plant diversity loss. Here, we compared the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in a subtropical tree diversity experiment. In addition to soil and spatial distance, plants are more strongly predictive of the community and co-occurrence network structure of fungi than those of bacteria. The study highlighted that plants play more important roles in shaping community assembly and interactions of fungi than of bacteria in the subtropical tree diversity experiment.

Soil Microbial Network Complexity Varies With pH as a Continuum, Not a Threshold, Across the North China Plain

There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequencing on a set of 90 samples across a 1,092 km transect in wheat fields of the North China Plain (NCP). We found that pH was the most important environmental factor driving network topology and relative abundance of keystone taxa. For the metacommunity composed of both bacteria and fungi, and for the bacterial community alone, lower soil pH was associated with a more complex microbial network. However, the network for fungi showed no strong trend with soil pH. In addition, keystone taxa abundance was positively correlated with ecosystem function and stability, and best explained by pH. Our results present new perspectives on impacts of pH on soil microbial network structure across large scales in agricultural environments. This improved knowledge of community processes provides a step toward understanding of functioning and stability of agricultural ecosystems.

Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession

Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this principle by identifying network-level topological features of the soil microbial co-occurrence networks in the primary successional foreland environment of the retreating high-Arctic glacier of Midtre Lovénbreen, Svalbard. Soil was sampled at sites along the foreland of inferred ages 10-90 years since deglaciation. DNA was extracted and amplicon sequenced for 16 s rRNA genes for bacteria and ITS1 region for fungi. Despite the chronologically-related soil pH decline and organic C/N accumulation, analysis on network-level topological features showed network integration did not change with inferred chronological ages, whereas network integration declined with decreasing pH and increasing total organic carbon (TOC) - both factors that can be viewed as an indicator of soil development. We also found that bacteria played a greater role in the network structure than fungi, with all keystone species in the microbial co-occurrence network being bacteria species. Both number and relative abundance of the keystone species were significantly higher when soil pH increased or TOC decreased. It appears that in the more extreme and less productive conditions of early primary succession, integration between members of soil biota into consortia may play a greater role in niche adaptation and survival. Our finding also emphasizes that ecosystem development is not simply a product of time but is influenced by locally heterogeneous factors.

Soil pH Filters the Association Patterns of Aluminum-Tolerant Microorganisms in Rice Paddies

Soil microbes are considered the second genome of plants. Understanding the distribution and network of aluminum (Al)-tolerant microorganisms is helpful to alleviate Al toxicity to plants in acidic soils. Here, we examined soluble Al³⁺ and bacterial communities carrying Al resistance genes in paddy soils with a soil pH range of 3.6 to 8.7. In the acidic soil with pH <5.1, the content of Al³⁺ increased significantly. There were abundant and diverse Al-tolerant microorganisms in acidic soils, including Clostridium, Bacillus, Paenibacillus, Desulfitobacterium, and Desulfosporosinus, etc. Moreover, compared with neutral and alkaline soils, the network structure of Al-tolerant microorganisms was more complex. The potential roles of major Al-tolerant microbial taxa on each other in the ecological network were identified by a directed network along 0.01 pH steps. The influential taxa in the network had a broader niche and contained more antioxidant functional genes to resist Al stress, indicating their survival advantage over the sensitive taxa. Our study is the first to explore the distribution of Al-tolerant microorganisms in continental paddies and reveal their potential associations mediated by pH, which provides a basis for further utilization of microbial resources in acidic agricultural soils. IMPORTANCE Aluminum (Al) toxicity is the primary limiting factor of crop production in acidic soils with pH <5.0. Numerous studies have focused on the mechanism of Al toxicity and tolerance in plants; however, the effects of Al toxicity on soil microorganisms and their tolerance remain less studied. This study investigated the distribution and association patterns of Al-tolerant microorganisms across continental paddy fields with a soil pH range of 3.6 to 8.7. The results showed that soil pH filters exchangeable Al³⁺ content, diversity, and potential associations of Al-tolerant microbial community. The influential taxa in community network play an important role in Al tolerance and have potential applications in mitigating Al toxicity and promoting crop growth in acidic soils.

Elevation-related climatic factors dominate soil free-living nematode communities and their co-occurrence patterns on Mt. Halla, South Korea

Nematodes play vital roles in soil ecosystems. To understand how their communities and coexistence patterns change along the elevation as well as to determine the best explanatory factors underlying these changes, we investigated free-living soil nematodes on Mt. Halla, South Korea, using an amplicon sequencing approach targeting the 18S rRNA gene. Our results showed that there was significant variation in the community diversity and composition of soil nematodes in relation to elevation. The network interactions between soil nematodes were more intensive at the lower elevations. Climatic variables were responsible explaining the elevational variation in community composition and co-occurrence pattern of the nematode community. Our study indicated that climatic factors served as the critical environmental filter that influenced not only the community structure but also the potential associations of soil nematodes in the mountain ecosystem of Mt. Halla. These findings enhance the understanding of the community structure and co-occurrence network patterns and mechanisms of soil nematode along elevation, and the response of soil nematodes to climate change on the vertical scale of mountain ecosystems.

Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice-Crab Co-culture System

Although co-culture of paddy fields with aquatic animals is lucrative, the ecological impacts of high-protein content entering the agricultural soil via animal pellet feed and feces have not been well studied. Moreover, the effects of dietary protein on soils and soil microbes remain unclear. To elucidate this, we examined soil bacterial and fungal community composition and temporal changes in paddy fields subjected to different protein-content diets via 16S/18S rRNA gene amplicon sequencing analysis with a high-throughput next-generation sequencer. MiSeq sequencing revealed that protein content significantly impacted fungal community structure. High-protein diets reduced bacterial community diversity and relative abundance in both July and October. The phylum-level bacterial taxonomic composition was not affected by diet treatment, while in fungi, a major phylum-level shift was evident. Hierarchically clustered analysis showed that high-protein diets significantly reduced the relative abundance of Brevundimonas in both July and October. Saprotrophic macrofungal diversity was negatively related to dietary protein content. Considering microbial community structure and environmental factors, ca. 15% protein content is appropriate for the rice-crab co-culture system that we studied.