Co-occurrence Network Structure Research Articles

Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems.

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Plant Secondary Compounds Promote White Adipose Tissue Browning via Modulation of the Gut Microbiota in Small Mammals.

The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.

Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival

Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands.

Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions. To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China. We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Performance and microbial community analysis of combined bioreactors in treating high–salinity hydraulic fracturing flowback and produced water

The anoxic/oxic systems are a widely used biological strategy for wastewater treatment. However, little is known about the performance and microbial community correlation of different combined bioreactors in the treatment of high-COD and high-salinity hydraulic fracturing flowback and produced water (HF-FPW). In this study, the performance of Up-flow anaerobic sludge bed-bio-contact oxidation reactor (UASB-BCOR) and Fixed-bed baffled reactor (FBR-BCOR) in treating HF-FPW was investigated and compared. The results suggested the FBR-BCOR could efficiently remove COD, SS, NH4+-N, and oil pollutants, and it exhibited better resistance to the negative interference of hydraulic shock load on it. Besides, the correlation analysis first disclosed the key functional genera during the degradation process, including Ignavibacterium, Ellin6067, and Zixibacteria. Moreover, network analysis revealed that the difference of microbial co-occurrence network structure is the main driving factor for the difference of bioreactor processing capacity. This work demonstrates the feasibility and potential of FBR-BCOR in treating HF-FPW.

Microbial mechanism of crop residues addition in nitrogen leaching loss retention and soil ecosystem stability maintenance

Over fertilization is the main factor in excessive N leaching (NL) loss in greenhouse vegetable cultivation systems. Adjusting the fertilizer application rate and returning plant residues effectively reduce NL. However, the microbial mechanism of crop residues addition in NL loss retention remains largely unknown. This study established a tomato-cultivating soil column experiment with different organic fertilizer addition treatments: no organic amendment (CK), chicken manure application (CM), chicken manure ＋rice husk (CMR), and chicken manure ＋maize straw (CMM) to further explore the discrepancies in the microbial community composition and the microbial co-occurrence network structure. The results revealed that CM produced the highest yield when provided with just enough nutrients for the crop requirements. The CMR yield decreased by 26.0%, while CMM remained at the same level as CK. Although discrepancies were evident between the decomposition characteristics and nutrient release rates of the rice husk and maize straw, no differences were apparent between the mineral NL loss retention of the two materials after one growing season, exhibiting a 47.8% and 50.4% reduction compared to CM. Furthermore, crop residues addition induced rapid microbial growth, increased the microbial community richness, and caused lignocellulose degraders accumulation, with fewer operational taxonomic units (OTUs) associated with the nitrification process. The CMM treatment produced a more robust and complex microbial co-occurrence network that was absent in the CM treatment. The results implied an alleviating effect of the straw amendment on mineral NL loss and emphasized the importance of readily available C sources in stabilizing an ecosystem.

Urbanization increases stochasticity and reduces the ecological stability of microbial communities in amphibian hosts.

Urbanization not only profoundly alters landscape profiles, ecosystems and vertebrate faunal diversity but also disturbs microbial communities by increasing stochasticity, vulnerability, biotic homogenization, etc. However, because of the buffering effect of host species, microbial communities are expected to be influenced by both host species and urbanization stresses. Therefore, the impacts of urbanization on animals' microbial symbionts could be more complex and uncertain. In this study, we quantified the urbanization degree of sampling sites and surveyed the gut and skin microbes of three amphibian host species in different sites in urban parks and nearby villages of Chengdu, Southwest China. Furthermore, a co-occurrence network analysis, the phylogenetic normalized stochasticity ratio and Sloan neutral community models were applied to infer the impact of urbanization on symbiotic microbial communities. For the three host species, urbanization increased the diversity of symbiotic microbes and the number of keystone microbial taxa. However, the negative effects of such increased diversification were evident, as the community stochasticity and co-occurrence network structure vulnerability also increased, while the network structure complexity and stability were reduced. Finally, the community stochasticity had positive associations with the network vulnerability, implying that the existence of many transient symbiotic rare microbial taxa in urban parks makes the symbiotic microbial community structure more fragile. Conclusively, urbanization increased the symbiotic microbial diversity at the cost of community stability; the results provide a new perspective for better understanding the complex triangulated environment-host-microbe relationship.

Application of malrstone-based conditioner and plantation of Jerusalem artichoke improved properties of saline-alkaline soil in Inner Mongolia

Soil salinization is a critical environmental issue restricting agricultural production. Inner Mongolia is one of the areas with severe land salinization in China. This study aimed to investigate the effects of conditioning agent (containing marlstone and a range of enzymes) and cultivating Jerusalem artichoke on saline soils in Inner Mongolia. The effects of conditioner (0, 0.06 and 0.18 kg/m2) on soil physical, chemical and biological properties, including soil carbon fractions and microbiota in saline soils planted with Jerusalem artichoke, were characterized. The results showed that soil salinity was reduced significantly after cultivating Jerusalem artichoke and declined also after the conditioner addition. The application of conditioner increased the content of DOC (dissolved organic carbon), HFOC (heavy fraction organic carbon) and the content of aggregates >0.25 mm compared to the soil planted with Jerusalem artichoke alone. The relative abundance of halophilic bacteria such as Thioalkalivibrio and Thiohalobacter was greater in the CK (non-treated control). By contrast, the relative abundance of microorganisms with the carbon assimilation and nitrogen fixation capacities, such as Cyanobacteria and Rhodovulum, was greater in the conditioner-treated and Jerusalem artichoke-planted treatments. The planting of Jerusalem artichoke reduced soil salinity, increased soil organic carbon fractions, improved soil structure, and altered the soil microbial community, with the application of the conditioning agent enhancing these positive changes. The co-occurrence network structure of “Jerusalem artichoke-conditioner-saline soil-soil microorganism” was established, which provided scientific basis for Jerusalem artichoke-conditioner to improve saline soil.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BackgroundSoil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.ResultsWe found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure.ConclusionsThe legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data

BackgroundStudying the co-occurrence network structure of microbial samples is one of the critical approaches to understanding the perplexing and delicate relationship between the microbe, host, and diseases. It is also critical to develop a tool for investigating co-occurrence networks and differential abundance analyses to reveal the disease-related taxa–taxa relationship. In addition, it is also necessary to tighten the co-occurrence network into smaller modules to increase the ability for functional annotation and interpretability of these taxa-taxa relationships. Also, it is critical to retain the phylogenetic relationship among the taxa to identify differential abundance patterns, which can be used to resolve contradicting functions reported by different studies.ResultsIn this article, we present Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA), a user-friendly R package for investigating compositional microbial sequencing data to identify and compare co-occurrence patterns across different taxonomic levels. C3NA contains two interactive graphic user interfaces (Shiny applications), one of them dedicated to the comparison between two diagnoses, e.g., disease versus control. We used C3NA to analyze two well-studied diseases, colorectal cancer, and Crohn’s disease. We discovered clusters of study and disease-dependent taxa that overlap with known functional taxa studied by other discovery studies and differential abundance analyses.ConclusionC3NA offers a new microbial data analyses pipeline for refined and enriched taxa–taxa co-occurrence network analyses, and the usability was further expanded via the built-in Shiny applications for interactive investigation.

The characterization of microbial communities and associations in karst tiankeng.

The karst tiankeng is a special and grand negative terrain on the surface, that maintains a unique ecosystem. However, knowledge about bacterial and fungal communities in karst tiankengs is still limited. Therefore, soil samples from five karst tiankengs were collected and subjected to high-throughput sequencing of 16S rRNA and ITS genes, and multivariate statistical analysis. The results showed abundant and diversified bacterial and fungal communities in karst tiankeng. The bacterial communities were dominated by Proteobacteria and Acidobacteria, and the fungal communities were dominated by Ascomycota and Basidiomycota. Statistical analysis revealed significant differences in bacterial and fungal communities among the five karst tiankengs, which may indicate that the distribution of bacterial and fungal communities was driven by separate karst tiankengs. The co-occurrence network structure was characterized by highly modularized assembly patterns and more positive interactions. The keystone taxa were mainly involved in nutrient cycling and energy metabolism. The null model analysis results showed that the stochastic process, especially dispersal limitation, tended to be more important in controlling the development of bacterial and fungal communities in karst tiankeng. The bacterial community structure was significantly associated with soil properties (SWC, TN, AN, and BD), while the fungal community structure was significantly associated with soil properties (SWC and TP) and plant diversity. These results can expand our knowledge of the karst tiankeng microbiome.

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil

BackgroundWeedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study.ResultsIn our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice.ConclusionsOur study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils.

Resilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradient

Wildfires can represent a major disturbance to ecosystems, including soil microbial communities belowground. Furthermore, fire regimes are changing in many parts of the world, altering and often increasing fire severity, frequency, and size. The boreal forest and taiga plains ecoregions of northern Canada are characterized by naturally-occurring stand-replacing wildfires on a 40–350 year basis. We previously studied the effects of wildfire on soil microbial communities one year post-fire across 40 sites, spanning a range of burn severity. Here, we return to the same sites five years post-fire to test a series of hypotheses about the effects of fire on bacterial community composition. We ask questions on two themes: which factors control bacterial community composition during post-fire recovery, and how does the importance of different fire-responsive traits change during post-fire recovery? We find the following: Five years post-fire, vegetation community, moisture regime, pH, total carbon, texture, and burned/unburned all remained significant predictors of bacterial community composition with similar predictive value (R2). Bacterial communities became more similar to unburned sites five years post-fire, across the range of severity, suggesting resilience, while general structure of co-occurrence networks remained similar one and five years post-fire. Fast growth potential, as estimated using predicted 16S rRNA copy numbers, was no longer significantly correlated with burn severity five years post-fire, indicating the importance of this trait for structuring bacterial community composition may be limited to relatively short timescales. Many taxa that were enriched in burned sites one year post-fire remained enriched five years post-fire, although the degree to which they were enriched generally decreased. Specific taxa of interest from the genera Massilia, Blastococcus, and Arthrobacter all remained significantly enriched, suggesting that they may have traits that allow them to continue to flourish in the post-fire environment, such as tolerance to increased pH or ability to degrade pyrogenic organic matter. This hypothesis-based work expands our understanding of the post-fire recovery of soil bacterial communities and raises new hypotheses to test in future studies.

Signatures of functional bacteriome structure in a tropical direct-developing amphibian species

BackgroundHost microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.ResultsIntensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.ConclusionsOur findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.

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

ABSTRACTIncreasing 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.

Depth-structuring of multi-kingdom soil communities in agricultural pastures.

The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1, 0.3-0.5, and1.1-1.7m)inpastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.

The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health.Key points• Swainsonine improves the intestinal bacterial diversity of plateau pikas.• Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas.• Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan

Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investigated the trend in co-occurrence network structure of soil fungal communities at 11 elevation levels along a 2300 m elevation gradient on Mt. Norikura, Japan, and identified the keystone taxa in the network, hypothesizing a progressive decline in network connectivity with elevation due to decreased plant diversity and enhanced environmental stress caused by changes in climate and soil characteristics. Our results demonstrated that network-level topological features such as network size, average degree, clustering coefficient, and modularity decreased significantly with increasing elevation, indicating that the fungal OTUs at low elevation were more closely associated and the network structure was more compact at low elevations. This conclusion was verified by the negative correlation between positive cohesion, negative cohesion and elevation. Moreover, the negative/positive cohesion ratio reached its peak value in mid-elevations with moderate environmental stress, indicating that the fungal community structure in mid-elevations was more stable than that at other elevations. We also found that the keystone taxa were more abundant at lower elevations. Furthermore, statistical analysis revealed that against a background of uniform geology, climate may play a dominant role in determining the properties and intensity of soil fungal networks, and significantly affect the abundance distribution of keystone taxa. These findings enhance understanding of the pattern and mechanism of the fungal community co-occurrence network along elevation, as well as the responses of microorganisms to climate change on a vertical scale in montane ecosystems. ImportanceExploration of the elevational distribution of microbial networks and their driving factors and mechanisms may provide opportunities for predicting potential impacts of environmental changes, on ecosystem functions and biogeographic patterns at a broad scale. Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts along elevational temperature gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Our results also suggest that higher elevations on mountains have fewer keystone taxa than low elevations. These patterns may be related to the decrease of plant diversity and the increase of environmental stress along elevation gradients.

Plant-plant co-occurrences under a complex land-use gradient in a temperate forest.

Land-use generates multiple stress factors, and we need to understand their effects on plant-plant interactions to predict the consequences of land-use intensification. The stress-gradient hypothesis predicts that the relative strength of positive and negative interactions changes inversely under increasing environmental stress. However, the outcome of interactions also depends on stress factor's complexity, the scale of analysis, and the role of functional traits in structuring the community. We evaluated plant-plant co-occurrences in a temperate forest, aiming to identify changes in pairwise and network metrics under increasing silvopastoral use intensity. Proportionally, positive co-occurrences were more frequent under high than low use, while negative co-occurrences were more frequent under low than high. Networks of negative co-occurrences showed higher centralization under low use, while networks of positive co-occurrences showed lower modularity and higher centralization under high use. We found a partial relationship between co-occurrences and key functional traits expected to mediate facilitation and competition processes. Our results shows that the stress-gradient hypothesis predicts changes in spatial co-occurrences even when two stress factors interact in a complex way. Networks of negative co-occurrences showed a hierarchical effect of dominant species under low use intensity. But positive co-occurrence network structure partially presented the characteristics expected if the facilitation was an important mechanism characterizing the community under high disturbance intensity. The partial relationship between functional traits and co-occurrences may indicate that other factors besides biotic interactions may be structuring the observed negative spatial associations in temperate Patagonian forests.