Microbial Co-occurrence Patterns Research Articles

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

Soil microbial community construction under revegetation in newly created land

Revegetation represents the primary method for restoring the ecological balance of the Loess Plateau. The assessment of revegetation efficacy on degraded lands can be facilitated through the utilization of soil microorganisms as indicators. We chose Medicago sativa L. (MX), Trifolium repens L. (BSY), Festuca arundinacea Schreb. (GYM), Elymus dahuricus Turcz. (PJC) and natural grass (CK) as the research objects, the soil microbial community composition, function and co-occurrence patterns of the five treatments were analyzed. The results showed that the microbial community composition was similar among the different vegetation types, but there were differences in abundance. Bacteria were significantly correlated with OM, BD and sand. Fungi were significantly correlated with sand and BD. Notably, BD showed highly significant correlation with microbial communities (P < 0.001). Microbial function prediction was dominated by metabolism at the bacterial level, and fungal function was predicted with eight trophic types dominated by parthenogenetic trophic types, and the microbial function prediction analyses showed that in bacteria, BSY had a high abundance of gene functions, and in fungi, PJC had a high abundance of gene functions. Network analysis revealed that the microbial community had small-world characteristics, a modular structure and a non-random co-occurrence pattern. Bacterial interactions included both competition and cooperation, further suggesting that growing raw grass increased the stability of the bacterial community. Overall, our results elucidated the changes in microbial communities and their correlations after raw grass cultivation, which could provide a more comprehensive perspective on microbial community assembly, and provide a theoretical basis for future ecological restoration on the Loess Plateau.

Long-term contamination of decabromodiphenyl ether reduces sediment multifunctionality: Insights from nutrient cycling, microbial ecological clusters, and microbial co-occurrence patterns

Despite the widespread detection of polybrominated diphenyl ethers in aquatic ecosystems, their long-term effects on sediment multifunctionality remain unclear. Herein, a 360-day microcosm experiment was conducted to investigate how decabromodiphenyl ether (BDE-209) contamination at different levels (0.2, 2, and 20 mg/kg dry weight) affects sediment multifunctionality, focusing on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling. Results showed that BDE-209 significantly increased sediment total organic carbon, nitrate, ammonium, available phosphorus, and sulfide concentrations, but decreased sulfate. Additionally, BDE-209 significantly altered key enzyme activities related to nutrient cycling. Bacterial community dissimilarity was positively correlated with nutrient variability. Long-term BDE-209 exposure inhibited C degradation, P transport and regulation, and most N metabolic pathways, but enhanced C fixation, methanogenesis, organic P mineralization, inorganic P solubilization, and dissimilatory sulfate reduction pathways. These changes were mainly regulated by microbial ecological clusters and keystone taxa. Overall, sediment multifunctionality declined under BDE-209 stress, primarily related to microbial co-occurrence network complexity and ecological cluster diversity. Interestingly, sediment C and N cycling had greater impacts on multifunctionality than P and S cycling. This study provides crucial insights into the key factors altering multifunctionality in contaminated sediments, which will aid pollution control and mitigation in aquatic ecosystems.

Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations

Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Distinct planting patterns exert legacy effects on the networks and assembly of root-associated microbiomes in subsequent crops

Soil legacy effects from previous crops can significantly influence plant–soil interactions in crop rotations. However, the microbial mechanism underlying this effect in subsequent root-associated compartments remains unclear. We investigated the effects of planting patterns (four-year continuous maize [MM], three-year winter wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, the effect of distinct crops on subsequent microbial co-occurrence patterns, and the assembly mechanism by which the root-associated compartments (bulk soil, rhizosphere, and roots) in subsequent crops regulate the microbiome habitat. Compared with MM, the relative abundance of Acidobacteria in WM was 29.7 % lower, whereas that of Bacteroidota in PM was 37.9 % higher in all three compartments. The co-occurrence patterns of the microbial communities exhibited varied responses to different planting patterns. Indicator taxon analysis revealed less shared and specific species in the root bacterial and fungal networks. The planting pattern elicited specific responses from modules within bacterial and fungal co-occurrence networks in all three compartments. Moreover, the planting patterns and root-associated compartments collectively drove the assembly process of root-associated microorganisms. The neutral model showed that, compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungal assembly. WM and PM increased the relative effects of the homogenized dispersal of fungal assemblies in roots. We conclude that previous crops exhibit marked legacy effects in the root-associated microbiome. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in subsequent crops.

Effect of Plateau pika on Soil Microbial Assembly Process and Co-Occurrence Patterns in the Alpine Meadow Ecosystem.

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats disturbed by Plateau pikas (Ochtona curzoniae). Pika disturbance had different impacts on bacterial and fungal communities. Fungal diversity generally increased with patch area, whereas bacterial diversity decreased. These strikingly different species-area relationships were closely associated with their community assembly mechanisms. The loss of bacterial diversity on larger patches was largely driven by deterministic processes, mainly due to the decline of nutrient supply (e.g., organic C, inorganic N). In contrast, fungal distribution was driven primarily by stochastic processes that dispersal limitation contributed to their higher fungal diversity on lager patches. A bacterial co-occurrence network exhibited a positive relationship of nodes and linkage numbers with patch area, and the fungal network presented a positive modularity-area relationship, suggesting that bacteria tended to form a closer association community under pika disturbance, while fungi tended to construct a higher modularity network. Our results suggest that pikas affects the microbial assembly process and co-occurrence patterns in alpine environments, thereby enhancing the current understanding of microbial biogeography under natural disturbances.

Linking phosphorus fertility to soil microbial diversity and network complexity in citrus orchards: Implications for sustainable agriculture

Continuous input of chemical fertilizers causes soil acidification, land degradation, and water eutrophication, but its impact on soil microbial communities and co-occurrence patterns of microboes is unclear. In this study, we evaluated the impact of chemical fertilizer on bacterial community diversity and ecological network at 75 citrus sites in a watershed where chemical fertilizer is continuously applied. In addition, 25 natural forest sites adjacent to citrus sites were used as references to compare the potential effects of land conversion from natural forests to citrus orchards on soil bacterial diversity and microbial network. The results showed that the cultivation of citrus results in soil phosphorus (P) accumulation, with significantly higher available and mineral-bound phosphate contents than those found in soils of natural forests. Citrus soil average soil available P was 73.2 mg/kg, which was 20 times higher than that in forest soils. As the P content accumulates, soil bacterial Shannon index linearly decreases from 7.06 to 5.93 and is significantly lower than that of adjacent natural forest soils (7.13). Low P fertility soils have higher microbial network complexity and stability, containing more microbial communities and tighter relationships between microbes compared to higher P fertility soils. Soil P content and soil pH regulates soil microbial network complexity and stability. In addition, soil bacterial community structure in soils of natural forests is significantly different from that in citrus soils, and the bacterial community structure in high P soils is different from that in medium and low P soils. Soil P fertility reduces the relative abundance of dominant communities including Proteobacteria, Bacteroidetes, and Gemmatimonadetes, and also changes the relative abundance of some functional microbial communities, such as some phosphorus cycling microorganisms, including Acetobacteraceae and Beijerinckiaceae. In conclusion, soil phosphate accumulation severely alters soil bacterial community diversity, complexity, stability, and functionality. This could have negative impacts on soil functional stability and the sustainability of citrus orchards.

Unraveling the ecological mechanisms of Aluminum on microbial community succession in epiphytic biofilms on Vallisneria natans leaves: Novel insights from microbial interactions

The extensive use of aluminum (Al) poses an escalating ecological risk to aquatic ecosystems. The epiphytic biofilm on submerged plant leaves plays a crucial role in the regulation nutrient cycling and energy flow within aquatic environments. Here, we conducted a mesocosm experiment aimed at elucidating the impact of different Al concentrations (0, 0.6, 1.2, 2.0 mg/L) on microbial communities in epiphytic biofilms on Vallisneria natans. At 1.2 mg/L, the highest biofilms thickness (101.94 µm) was observed. Al treatment at 2.0 mg/L significantly reduced bacterial diversity, while micro-eukaryotic diversity increased. Pseudomonadota and Bacteroidota decreased, whereas Cyanobacteriota increased at 1.2 mg/L and 2.0 mg/L. At 1.2 and 2.0 mg/L. Furthermore, Al at concentrations of 1.2 and 2.0 mg/L enhanced the bacterial network complexity, while micro-eukaryotic networks showed reduced complexity. An increase in positive correlations among microbial co-occurrence patterns from 49.51% (CK) to 57.05% (2.0 mg/L) was indicative of augmented microbial cooperation under Al stress. The shift in keystone taxa with increasing Al concentration pointed to alterations in the functional dynamics of microbial communities. Additionally, Al treatments induced antioxidant responses in V. natans, elevating leaf reactive oxygen species (ROS) content. This study highlights the critical need to control appropriate concentration Al concentrations to preserve microbial diversity, sustain ecological functions, and enhance lake remediation in aquatic ecosystems.

Microbial survival strategies in biological soil crusts of polymetallic tailing wetlands

The role of biological soil crusts (biocrusts) in ecological restoration is dominated by microbiota. This has been extensively studied in arid ecosystems characterized by nutrient deficiencies and poor soil substrates, including metal(loid)-rich mining regions. However, in the prior study areas, water constraints obscured the toxicity and restriction of succession by heavy metals, which were essential for soil remediation in mining regions using biocrusts. Accordingly, in the current study, we characterized biocrusts from a typical polymetallic tailing wetland and performed pot incubation to evaluate microbial community succession and microbial co-occurrence patterns. Results showed that adequate water and heavy-metal stress produced thicker and more hydrophobic biocrusts than did arid conditions, promoting stronger microbial activity in tailing wetlands. Moreover, the bioinformatic analyses during pot incubation suggest three potential survival strategies. (1) Cyanobacteria variation improved the succession level of cyanobacterial crusts. Even under heavy-metal stress, succession from light to dark cyanobacterial crusts still occurred, with Coleofasciculaceae decreasing 63% and Scytonema increasing 59% compared with the control groups. (2) Keystone taxa variation maintained high inorganic nitrogen turnover. Organisms potentially capable of inorganic nitrogen turnover, including Chloroflexi A4b and SBR1031, maintained a high relative abundance accounting for 42% (15/36) of the keystone taxa. (3) Variations in the interactions among microbiota created closer-knit microbial networks. Compared with the control groups, fewer nodes (15.2%) maintained higher average clustering coefficient values (1.8%) through 14% more positive interactions in the groups exposed to heavy-metal stress at the end of the incubation experiment. This study provides insights into the distinctive survival strategies of biocrusts in metal-rich extreme environments, offering theoretical support for biocrust-mediated ecological restoration in humid metal-contaminated regions.

Biotic and abiotic factors interplay in structuring the dynamics of microbial co-occurrence patterns in tropical mountainsides

Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO43--P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient.

Effect of aridity on the β-diversity of alpine soil potential diazotrophs: insights into community assembly and co-occurrence patterns.

Microbial diversity plays a vital role in the maintenance of ecosystem functions. However, the current understanding of mechanisms that shape microbial diversity along environmental gradients at broad spatial scales is relatively limited, especially for specific functional groups, such as potential diazotrophs. Here, we conducted an aridity-gradient transect survey from 60 sites across the Tibetan Plateau, the largest alpine ecosystem of the planet, to investigate the ecological processes (e.g., local species pools, community assembly processes, and co-occurrence patterns) that underlie the β-diversity of alpine soil potential diazotrophic communities. We found that aridity strongly and negatively affected the abundance, richness, and β-diversity of soil diazotrophs. Diazotrophs displayed a distance-decay pattern along the aridity gradient, with organisms living in lower aridity habitats having a stronger distance-decay pattern. Arid habitats had lower co-occurrence complexity, including the number of edges and vertices, the average degree, and the number of keystone taxa, as compared with humid habitats. Local species pools explained limited variations in potential diazotrophic β-diversity. In contrast, co-occurrence patterns and stochastic processes (e.g., dispersal limitation and ecological drift) played a significant role in regulating potential diazotrophic β-diversity. The relative importance of stochastic processes and co-occurrence patterns changed with increasing aridity, with stochastic processes weakening whereas that of co-occurrence patterns enhancing. The genera Geobacter and Paenibacillus were identified as keystone taxa of co-occurrence patterns that are associated with β-diversity. In summary, aridity affects the co-occurrence patterns and community assembly by regulating soil and vegetation characteristics and ultimately shapes the β-diversity of potential diazotrophs. These findings highlight the importance of co-occurrence patterns in structuring microbial diversity and advance the current understanding of mechanisms that drive belowground communities.IMPORTANCERecent studies have shown that community assembly processes and species pools are the main drivers of β-diversity in grassland microbial communities. However, co-occurrence patterns can also drive β-diversity formation by influencing the dispersal and migration of species, the importance of which has not been reported in previous studies. Assessing the impact of co-occurrence patterns on β-diversity is important for understanding the mechanisms of diversity formation. Our study highlights the influence of microbial co-occurrence patterns on β-diversity and combines the drivers of community β-diversity with drought variation, revealing that drought indirectly affects β-diversity by influencing diazotrophic co-occurrence patterns and community assembly.

Linking the impact of bacteria on phytoplankton growth with microbial community composition and co-occurrence patterns

The interactions between microalgae and bacteria have recently emerged as key control factors which might contribute to a better understanding on how phytoplankton communities assemble and respond to environmental disturbances. We analyzed partial 16S rRNA and 18S rRNA genes from a total of 42 antibiotic bioassays, where phytoplankton growth was assessed in the presence or absence of an active bacterial community. A significant negative impact of bacteria was observed in 18 bioassays, a significant positive impact was detected in 5 of the cases, and a non-detectable effect occurred in 19 bioassays. Thalasiossira spp., Chlorophytes, Vibrionaceae and Alteromonadales were relatively more abundant in the samples where a positive effect of bacteria was observed compared to those where a negative impact was observed. Phytoplankton diversity was lower when bacteria negatively affect their growth than when the effect was beneficial. The phytoplankton-bacteria co-occurrence subnetwork included many significant Chlorophyta-Alteromonadales and Bacillariophyceae-Alteromonadales positive associations. Phytoplankton-bacteria co-exclusions were not detected in the network, which contrasts with the negative effect of bacteria on phytoplankton growth frequently detected in the bioassays, suggesting strong competitive interactions. Overall, this study adds strong evidence supporting the key role of phytoplankton-bacteria interactions in the microbial communities.

Depth significantly affects plastisphere microbial evenness, assembly and co-occurrence pattern but not richness and composition

Microplastics have become one of the hot concerns of global marine pollution. In recent years, diversity and abiotic influence factors of plastisphere microbial communities were well documented, but our knowledge of their assembly mechanisms and co-occurrence patterns remains unclear, especially the effects of depth on them. Here, we collected microorganisms on microplastics to investigate how ocean depth affects on microbial diversity, community composition, assembly processes and co-occurrence patterns. Our results indicated that there were similar microbial richness and community compositions but microbial evenness and unique microbes were obviously different in different ocean layers. Our findings also demonstrated that deterministic processes played dominant roles in the assembly of the mesopelagic plastisphere microbial communities, while the bathypelagic microbial community assembly was mainly shaped by stochastic processes. In addition, the co-occurrence networks suggested that the relationships between microorganisms in the mesopelagic layer were more complex and stable than those in the bathypelagic layer. Simultaneously, we also found that Proteobacteria and Actinobacteriota were the most abundant keystones which played important roles in microbial co-occurrence networks at both layers. This study enhanced our understanding of microbial diversity, assembly mechanism, and co-occurrence pattern on plastisphere surfaces, and provided useful insights into microorganisms capable of degrading plastics and microbial remediation.

Wheat cultivar replacement drives soil microbiome and microbial cooccurrence patterns

While wheat domestication is reported to influence the soil microbial community, few studies have evaluated the influence of cultivar replacement in modern breeding on both bacterial and fungal communities. Especially, few studies reported the bacterial-fungal interkingdom association by analysis of taxa co-occurrence or co-exclusion between different wheat growth stages. In this study, we selected major wheat cultivars from different decades to investigate their genetic relatedness, plant traits, soil bacterial and fungal communities in the rhizosphere and proximal root zone, and the relationships between them. Our results indicated that host selection had the greatest impact on bacterial and fungal communities compared to growth stage and sampling location (P<0.001). At flowering, the soil microbial community in the genotype group consisting of the 1950 s (W50 s) and 1960 s (W60 s) cultivars could be clearly distinguished from those in later genotype groups. Plant traits explained the largest source of variation in microbial β-diversity (12.8–20.6%) (P=0.01), with plant height, aboveground dry matter, leaf area per plant and specific root length being associated with the divergence in microbial composition or quantity among cultivars. The cultivar from the 1970 s (W70 s) enriched a greater number of microbial taxa with the highest relative abundance, suggesting that old cultivar could be considered as a source of cultivar-microbe interaction. The cultivar from the 2000 s (W00 s) enriched taxa from the bacterial genus Nocardioides and increased the fungal phylum Glomeromycota in the rhizosphere. At three growth stages, W00 s root-zone exhibited the highest bacteria/fungi ratio (B/F) and contained more phosphorus cycle-related bacterial phoD-genes than W50 s and W60 s. The co-occurrence network revealed more operational taxonomic units (OTUs) from the bacterial order Rhizobiales in the largest module of W00 s. The increased B/F ratio and the aforementioned taxa are reported to be involved in soil nitrogen and phosphorus availability, suggesting that contemporary cultivar may recruit beneficial bacteria and fungi while weaken the association with other fungi. These findings contribute to the development of microbiome-based breeding strategies for sustainable wheat farming.

Micro-nano bubble water with potassium fertigation improves strawberry yield and quality by changing soil bacterial community

Aerated drip irrigation can increase the soil oxygen content and improve the utilization efficiency of fertilizer. However, limited information is available on how soluble potassium fertilizer with different aeration levels affects plant yield and quality. Specifically, the underlying mechanism associated with microbial community level has not been reported so far. In this study, a micro-nano bubble water (MNBW) drip irrigation experiment was conducted in a strawberry plantation greenhouse, with three ratios of MNBW and two potassium application amounts and a control treatment (without MNBW). The results showed that compared with the CK (no aeration, 100% traditional potassium fertilizer application, 144 kg hm−2 of potassium sulfate), MNBW irrigation improved the soil oxygen content and changed the structure and functionality of the soil microbial community in the strawberry rhizosphere. The bacterial diversity was reduced, and the microbial co-occurrence patterns were altered. The soil respiration intensity increased by 1.32%–14.22%. The soil temperature increased, and the decomposition of organic matter was enhanced. It was indicated that the increase of soil oxygen had a positive impact on soil fertility, strawberry yield, and quality under the condition of reducing potassium application. The yield and quality of strawberries in MNBW treatments were significantly higher than those treated with CK (p < 0.05), but the carbon dioxide emissions significantly increased. High potassium fertilizer application amount and MNBW ratio did not mean high yield and quality of strawberries. Thus, O20K70 (20% of irrigation water with micro-nano bubbles, 70% of traditional drip irrigation potassium fertilizer level, 101 kg hm−2 of potassium sulfate) and O60K70 (60% of irrigation water with micro-nano bubbles, 70% of traditional drip irrigation potassium fertilizer level, 101 kg hm−2 of potassium sulfate) could be chosen for strawberry plantations with MNBW.

Abundant and rare fungal taxa exhibit different patterns of phylogenetic niche conservatism and community assembly across a geographical and environmental gradient

Fungi play critical roles in the regulation of terrestrial ecosystem processes and functions. However, the biogeographic patterns, assembly mechanism and phylogenetic information of fungi across complex environmental gradients remains unexplored, especially the differences between abundant and rare fungi. Here, based on an extensive soil sampling (117 samples) covering almost all vegetation types in the Loess Plateau, we explored biogeography, community assembly, and phylogenetic niche conservatism of abundant and rare fungi. The results showed that the abundant fungal taxa exhibited less phylogenetic clustering than the rare fungi, but their environmental associations and phylogenetic signals were stronger. Stochastic processes dominated the assembly of abundant fungi. In contrast, the homogeneous selection of deterministic processes was the major assembly process of rare taxa. Soil organic carbon and nitrate nitrogen were the key factors driving the community assembly of abundant and rare fungi, respectively. Microbial network and niche analyses further indicated abundant fungi were more advantageous for maintaining microbial co-occurrence patterns and metabolic flexibility. We concluded that abundant fungi have broader environmental adaptation potential at spatially complex environmental scales and are less dispersed by environmental changes. These results provide insights for understanding the phylogenetic and community assembly mechanisms by which fungi adapt to large-scale environmental changes.

Mechanisms by which chloropicrin fumigation promotes soil potassium conversion and absorption.

Fumigation of soil using chloropicrin has been proven to significantly affect soil nutrient cycling, but the mechanism by which soil potassium conversion and plant uptake is promoted remains unclear. In this study, we conducted a fumigation experiment to investigate the effects of chloropicrin soil fumigation on the conversion of soil potassium post-fumigation (days 7-70), and its mechanisms, tomatos were planted in fumigated and non-fumigated soils to enable further comparisons. Results showed that the content of rapidly available potassium and available potassium decreased by 16-24% and 17-23% at day 28 respectively, when tomato was planted in chloropicrin-fumigated soils compared to the non-fumigated soils. The potassium content of tomato planted in fumigated soil was significantly higher than that planted in non-fumigated soil (30.3 vs. 21.9 mg g-1 dry weight). Chloropicrin fumigation resulted in a significant change in the soil bacterial and fungal community structures, and trigged a long-term (at least 70-day) decrease in microbial diversity. Network analysis showed that chloropicrin soil fumigation changed microbial co-occurrence patterns by decreasing bacterial total links, nodes, and average degree, and increasing fungal total links, nodes, and average degree. Chloropicrin fumigation caused significant changes in the relative abundance of Bacillus species, which are involved in potassium dissolution. Structural equation model (SEM) suggested that fumigation with chloropicrin enhanced the contribution of soil potassium to tomato growth and reduced the contribution of bacterial communities. Together, the results of our study help in understanding the crop yield enhancement mechanism of soil fumigation.

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67–14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery.

Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Our results suggested soil microbial a-diversity decreased under high C10-C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10-C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.