Soil Microbial Networks Research Articles

Petroleum‐contamination drives the shift of microbiome through modifying soil metallome

AbstractSoil oil‐pollution is one of the most severe environmental issues at present. Shifts of soil metallome and microbiome are essential indicators for risk assessment and remediation of field soil pollutions. However, how soil metallome and microbiome react to petroleum‐contamination is not well studied. In this research, soil samples were collected from a short‐term and long‐term petroleum‐contaminated oil field. The soil physicochemical properties, metallome, microbiome, and soil microbial networks were investigated. Results showed that the contents of soil total petroleum hydrocarbon, total carbon, total nitrogen, total sulfur, total phosphorus, calcium, copper, manganese, lead, and zinc were increased by petroleum‐contamination because petroleum is rich in these elements. In contrast, the soil pH was lowered resulting from soil sulfur oxidation regardless of the petroleum pollution duration. Petroleum‐contamination also reduced bacterial and fungal α‐diversity indices because of the selective pressure of petroleum. Furthermore, bacterial α‐diversity was negatively correlated with soil total petroleum hydrocarbon content and electrical conductivity, and fungal α‐diversity was negatively correlated with soil electrical conductivity. Moreover, the relative abundances of Proteobacteria, Ascomycota, Oleibacter, and Fusarium in soil were increased by petroleum‐contamination. Network analysis showed that number of links, modules, and the network invulnerability decreased in short‐term contaminated soil, followed by the long‐term contaminated group, and the main reason should be the environmental disturbance caused by petroleum‐contamination. These results demonstrate that short‐term heavy petroleum contamination can cause shifts in soil physicochemical properties, metallome, and microbiome and assemble a less complex and vulnerable soil microbial network. Moreover, natural restoration can hardly amend soil properties and microbial network structure. This research emphasizes that the uncommonly studied soil metallome may play a vital part in the reaction of microbial communities to petroleum‐contamination.

Microplastics reduce soil microbial network complexity and ecological deterministic selection.

Microplastics have been proposed as emerging threats for terrestrial systems as they may potentially alter the physicochemical/biophysical soil environments. Due to the variety of properties of microplastics and soils, the microplastic-induced effects in soil ecosystems are greatly manifold. Here, we studied effects of three polymer microplastics (polyamide-6, polyethylene, and polyethylene terephthalate) on soil properties with four different soil types. The success patterns, interaction relationships, and assembly processes of soil bacterial communities were also studied. Microplastics have the potential to promote CO2 emissions and enhance the soil humification. Even though microplastics did not significantly alter the diversity and composition of the soil microbial community, the application of microplastics decreased the network complexity and stability, including network size, connectivity, and the number of module and keystone species. The bacterial community assembly was governed by deterministic selection (77.3%-90.9%) in all treatments, while microplastics increased the contribution of stochastic processes from 9.1% in control to 13.6%-22.7%. The neutral model results also indicated most of the bacterial taxa were present in the predicted neutral region (approximately 98%), suggesting the importance of stochastic processes. These findings provided a fundamental insight in understanding the effects of microplastics on soil ecosystems.

Network complexity of rubber plantations is lower than tropical forests for soil bacteria but not for fungi

Abstract. Soil microbial communities play a crucial role in ecosystem functioning. Past research has examined the effects of forest conversion on soil microbial composition and diversity, but it remains unknown how networks within these communities respond to forest conversion, including when tropical rainforests are replaced with rubber plantations. Microbial networks are viewed as critical indicators of soil health and quality. They consist of two parts: nodes and edges. In this study, we used data from Illumina sequencing and shotgun metagenome sequencing to analyze bacterial and fungal community network structure in a large number of soil samples from tropical rainforests and rubber plantation sites on Hainan Island, China. Our results showed that only 5 %–10 % of shared network edges (i.e., links between species A and B existing in both rubber plantations and rainforests) were observed in both bacterial and fungal communities, which indicates that forest conversion altered the soil microbial network structure. The identity of keystone operational taxonomic units (OTUs) differed entirely between rubber plantation and rainforest sites, further underscoring the altered network structure. More edges and more negative correlations within the soil bacterial–fungal networks were observed at rubber plantation sites (dry season: 4284 total edges, 844 negative; rainy season: 7257 total edges, 1744 negative) than at rainforest sites (dry season: 3650 total edges, 149 negative; rainy season: 6018 total edges, 489 negative), demonstrating that soil bacterial–fungal network structure was more complex and stable in rubber plantations than in rainforests. For bacteria, a larger number of network edges were observed among bacterial networks in samples from tropical rainforest than in samples from rubber plantations, indicating that rainforest bacterial networks were more complex than those from rubber plantations. However, soil fungal networks from rubber plantations showed more links, suggesting that forest conversion increased fungal network complexity. More edges of network and more links between species and functions were observed in the rainy season than in the dry season, indicating that seasonal changes had a strong effect on network structure and function. Further analysis shows that soil pH, potassium (AK), and total nitrogen (TN) had more links with species of some phyla. In conclusion, forest conversion results in an increase in soil pH as well as a decrease in AK and TN, and these changes as well as seasonal variations had a great impact on soil microbial composition, network structure and function.

Biogeographic patterns of soil microbe communities in the deserts of the Hexi Corridor, northern China

Recent studies show that different microorganisms, especially bacteria and fungi, exhibit contrasting latitudinal, longitudinal, and altitudinal diversity patterns at a global scale, but little is known about biogeographic patterns in desert ecosystems. In this study, we chose a narrow geographic channel, namely the deserts of northern China’s Hexi Corridor as the study area. Based on field survey and next-generation sequencing (Illumina MiSeq PE300 Platform), to map soil microbial geographic diversity patterns in this area and further determine the main driving factors responsible for shaping the soil microbial community. The results show that bacteria and eukaryotic diversity increased linearly with increasing longitude and altitude, but decreased with increasing latitude in the Hexi Corridor deserts, whereas archaeal diversity showed little change along these geographic gradients. Some individual phyla within the bacterial, archaeal, and eukaryota communities were not always consistent with collective trends, e.g., for the α-diversity of the ten most dominant bacterial phyla, only six phyla showed a statistically significant increase with altitude. The soil microbial community composition was jointly shaped by geographic distance and environmental variables (regional climatic factors and local edaphic variables). The effect of geographic distance on the soil microbial community composition was slightly stronger than that of the environmental variables. Intra-domain links were stronger than inter-domain links in the soil microbial network of the Hexi Corridor deserts, and these links were mostly positive. Although bacteria formed more connections than both archaea and eukaryotes, removing the archaea resulted in a lower natural connectivity, suggesting that the archaea were the core group for building this desert region’s soil microbial co-occurrence network. Taken together, these findings deepen our understanding of regional-scale soil microbial diversity patterns in this desert ecosystem.

Tree decline and mortality following pathogen invasion alters the diversity, composition and network structure of the soil microbiome

The loss of tree health is a global concern with many unknown cascading impacts on the diversity and function of forest ecosystems. Specifically, it is uncertain how the process of tree decline and mortality driven by exotic pathogens might alter the soil microbiome. Here we combined high-throughput sequencing, neighborhood models, and network analysis to explore the impacts of the decline of a Mediterranean tree species, Quercus suber, on the diversity, composition and network structure of soil fungal and bacterial communities in forests invaded by the exotic pathogen Phytophthora cinnamomi. The belowground footprint of pathogen-driven tree decline implied an increase in the taxonomic and phylogenetic diversity of both bacteria and fungi, but also a severe reduction of tree-symbiotic fungi and Proteobacteria known to have positive effects on plant growth and disease suppression. Moreover, we detected alterations of the topology of soil microbial networks in declining tree neighborhoods (lower connectivity, higher modularity), with implications for ecosystem function. Our findings reveal the large impacts that moderate levels of tree decline can have on the soil microbiome of invaded forests, and highlight the recovery of a functionally diverse and highly connected soil microbiome as a key target in the restoration of these disturbed systems.

Intercropping Systems Modify Desert Plant-Associated Microbial Communities and Weaken Host Effects in a Hyper-Arid Desert.

Intercropping is an important practice in promoting plant diversity and productivity. Compared to the accumulated understanding of the legume/non-legume crop intercrops, very little is known about the effect of this practice when applied to native species on soil microbial communities in the desert ecosystem. Therefore, in the present study, bulk soil and rhizosphere microbial communities in the 2-year Alhagi sparsifolia (legume)/Karelinia caspica (non-legume) monoculture vs. intercropping systems were characterized under field conditions. Our result revealed that plant species identities caused a significant effect on microbial community composition in monocultures but not in intercropping systems. Monoculture weakened the rhizosphere effect on fungal richness. The composition of bacterial and fungal communities (β-diversity) was significantly modified by intercropping, while bacterial richness (Chao1) was comparable between the two planting patterns. Network analysis revealed that Actinobacteria, α- and γ-proteobacteria dominated bulk soil and rhizosphere microbial co-occurrence networks in each planting pattern. Intercropping systems induced a more complex rhizosphere microbial community and a more modular and stable bulk soil microbial network. Keystone taxa prevailed in intercropping systems and were Actinobacteria-dominated. Overall, planting patterns and soil compartments, not plant identities, differentiated root-associated microbiomes. Intercropping can modify the co-occurrence patterns of bulk soil and rhizosphere microorganisms in desert ecosystems. These findings provided a potential strategy for us to manipulate desert soil microbial communities and optimize desert species allocation in vegetation sustainability.

Short-term cellulose addition decreases microbial diversity and network complexity in an Ultisol following 32-year fertilization

Cellulose is an essential component of plant cell walls, and one of the major constituents of soil organic matter. Decomposition of cellulose, mediated by microorganisms, is critical to the sustainable development of arable soils. However, how exogenous cellulose addition, as a surrogate for organic material amendment, influences the diversity and community compositions of soil microorganisms and their network complexity remains largely unknown. To bridge this knowledge gap, we conducted a microcosm experiment incubated with soils that had been subjected to long-term mineral or organic fertilization. Cellulose addition increased the cumulative CO2 emission in all treatments, with the highest value found in the pig manure amended soils. Cellulose addition significantly reduced the alpha diversity of bacteria and fungi across all fertilization treatments, with a more pronounced effect observed for fungi. Moreover, cellulose addition strongly altered bacterial community structure by increasing the relative abundance of copiotrophic bacteria such as Actinobacteria and Proteobacteria while reducing that of oligotrophic bacteria (e.g., Chloroflexi). Compared with no-fertilizer treatment, the influence of cellulose addition on bacterial and fungal community structure was stronger in long-term mineral or organic fertilized soils. Cellulose addition altered the relative abundance of bacterial and fungal functional groups by generally enriching microbes involved in chemoheterotrophy and suppressing those involved in methylotrophy, pathotroph, saprotroph-symbiotroph, and saprotroph-pathotroph. In addition, cellulose addition decreased soil microbial complexity and the number of potential keystone species, but did not change the key role of Chloroflexi in soil microbial network. Overall, our results demonstrated that cellulose addition decreased soil microbial diversity and network complexity, with possible short-term negative consequences for ecosystem functioning in Ultisols.

Reflections and Insights on the Evolution of the Biological Remediation of Contaminated Soils

The field of soil biological remediation was initially focused on the use of microorganisms. For organic contaminants, biostimulation and bioaugmentation were the strategies of choice. For heavy metals, bioremediation was centered on the feasibility of using microorganisms to reduce metal toxicity. Partly due to the impossibility to degrade metals, phytoremediation emerged proposing the use of plants to extract them (phytoextraction) or reduce their bioavailability (phytostabilization). Later, microbial-assisted phytoremediation addressed the inoculation of plant growth-promoting microorganisms to improve phytoremediation efficiency. Similarly, plant-assisted bioremediation examined the stimulatory effect of plant growth on the microbial degradation of soil contaminants. The combination of plants and microorganisms is nowadays often recommended for mixed contaminated soils. Finally, phytomanagement emerged as a phytotechnology focused on the use of plants and associated microorganisms to decrease contaminant linkages, maximize ecosystem services, and provide economic revenues. Although biological remediation methods have been in use for decades, the truth is that they have not yet yielded the expected results. Here, we claim that much more research is needed to make the most of the many ways that microorganisms have evolutionary developed to access the contaminants and to better understand the soil microbial networks responsible, to a great extent, for soil functioning.

Biochar-based fertilizer amendments improve the soil microbial community structure in a karst mountainous area

Biochar-based fertilizer amendment can improve soil properties partly due to stimulated microbial activities and growths. The karst ecosystem is prone to degradation and accounts for a large proportion of southwest China. Understanding of the response of the microbial community structure to biochar-based fertilizer application is of great significance in karst soil restoration. A field experiment located in southwest China was conducted in typical karst soil, and a high-throughput sequencing approach was used to investigate the effect of biochar-based fertilizer application on microbial community structure in karst soil. Field trials were set up for 24 months using the following treatments: control (CK), compost plus NPK fertilizer (MF), biochar (B), less biochar (half the quantity of biochar in B) plus compost and NPK fertilizer (B1MF), biochar plus compost and NPK fertilizer (BMF), and more biochar (double the quantity of biochar in B) plus compost and NPK fertilizer (B4MF). The results elucidated that BMF and B4MF treatments had higher contents of soil carbon and soil nutrients N, P, and K than the other treatments. Soil microbial abundance and diversity were significantly increased by biochar-based fertilizer amendments (BMF and B4MF), compared to CK (P < 0.05). BMF and B4MF treatments significantly increased the relative abundance of dominant microorganisms, compared to CK (P < 0.05). The difference in the composition of indicator microbes between each treated group indicated that soil amendments altered the microbial community structure. There was a strong correlation between soil properties (soil C-, N-, and P-fractions) and microbial community structure. Furthermore, network analysis revealed that the addition of biochar-based fertilizer increased the scale and complexity of the microbial co-occurrence network. To summarize, the application of biochar-based fertilizer enabled more keystone species in the soil microbial network to participate in soil carbon resource management and soil nutrient cycling, indicating that biochar-based fertilizer is beneficial for the restoration of karst-degraded soils.

Pulse Frequency in Crop Rotations Alters Soil Microbial Community Networks and the Relative Abundance of Fungal Plant Pathogens.

Including pulse crops in cereal-based cropping systems has become a widely accepted and useful agronomic practice to increase crop diversification and biologically fixed nitrogen in agroecosystems. However, there is a lack of knowledge regarding how the intensification of pulses in crop rotations influence soil microbial communities. In this study, we used an amplicon sequencing approach to examine the bulk and rhizosphere soil bacterial and fungal communities from the wheat (Triticum aestivum L.) phase (final year of 4 years rotations) of a long-term pulse intensification field trial in the semi-arid region of the Canadian Prairies. Our results revealed pulse frequency had a minimal impact on microbial α-diversity, but caused a significant shift in the composition of the fungal (rhizosphere and bulk soil) and bacterial (bulk soil) communities. This effect was the most pronounced in the Ascomycete and Bacteroidete communities. Increasing pulse frequency also promoted a higher proportion of fungal pathotrophs in the bulk soil, particularly those putatively identified as plant pathogens. The network analysis revealed that rotations with higher pulse frequency promoted increased competition within the soil microbial networks in the rhizosphere and bulk soil. However, we also detected more negative interactions among the dominant pathotrophic taxa with increased pulse frequency, suggesting higher soil-borne disease potential. These findings highlight the potential drawbacks and reduced sustainability of increasing pulse frequency in crop rotations in semiarid environments.

Robustness of rhizosphere microbial communities of L. sativa originated from soils of different legacy after inoculation with Plant Growth Promoting Rhizobacteria

Organic and conventional agricultural systems present differences in soil microbial biomass, activity and community composition. However, data concerning the network of correlations among the microbial members in agricultural soils are too limited. In this paper, we examined structural characteristics of the network of these correlations developed in two soils of different legacy (an organic maize (O) and a conventional barley cultivation (C)) cultivated with lettuce (Lactuca sativa L.) plants in a pot experiment. Further, in each soil, inoculation with Plant Growth Promoting Rhizobacteria (PGPR) took place once: Bacillus subtilis (Ba; gram-positive), Pseudomonas fluorescens (Ps; gram-negative), both inoculants (Ps + Ba) and a control without inoculants. We considered inoculation as perturbations for the rhizosphere soil microbes and we estimated the robustness of the soil microbial networks denoting their ability to retain connectivity. Networks from all treatments exhibited positive values of modularity, small-worldness index (SW) >1 and clustering coefficient > 0.4, indicating modular structure, small world properties and the predominance of direct connections. The network in C control exhibited higher values of density and centrality and lower values of fragmentation and SW compared to O control. In organic system, the highest fragmentation (0.55 and 0.62) and SW values (4.98 and 5.48) were in control and co-inoculated soils respectively while in conventional system the highest values were in soils with Ba or Ps inoculants; fragmentation 0.52 (Ba) and 0.48 (Ps), SW 3.54 (Ba) and 4.14 (Ps). The robustness of the soil microbial communities depended on soil legacy (prior management system) as well as whether each inoculant applied individually or jointly, while the type of inoculant was insignificant.

Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems

Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities

The use of synthetic pesticides in agriculture is increasingly debated. However, few studies have compared the impact of synthetic pesticides and alternative biopesticides on non-target soil microorganisms playing a central role in soil functioning.We conducted a mesocosm experiment and used high-throughput amplicon sequencing to test the impact of a fungal biopesticide and a synthetic fungicide on the diversity, the taxonomic and functional compositions, and co-occurrence patterns of soil bacterial, fungal and protist communities.Neither the synthetic pesticide nor the biopesticide had a significant effect on microbial α-diversity. However, both types of pesticides decreased the complexity of the soil microbial network. The two pesticides had contrasting impacts on the composition of microbial communities and the identity of key taxa as revealed by microbial network analyses. The biopesticide impacted keystone taxa that structured the soil microbial network. The synthetic pesticide modified biotic interactions favouring taxa that are less efficient at degrading organic compounds. This suggests that the biopesticides and the synthetic pesticide have different impact on soil functioning.Altogether, our study shows that pest management products may have functionally significant impacts on the soil microbiome even if microbial α-diversity is unaffected. It also illustrates the potential of high-throughput sequencing analyses to improve the ecotoxicological risk assessment of pesticides on non-target soil microorganisms.

Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem.

Understanding microbial network assembly is a promising way to predict potential impacts of environmental changes on ecosystem functions. Yet, soil microbial network assembly in mountain ecosystems and its underlying mechanisms remain elusive. Here, we characterized soil microbial co-occurrence networks across 12 altitudinal sites in Mountain Gongga. Despite differences in habitats, soil bacterial networks separated into two different clusters by altitude, namely the lower and higher altitudes, while fungi did not show such a pattern. Bacterial networks encompassed more complex and closer relationships at the lower altitudes, while fungi had closer relationships at the higher altitudes, which could be attributed to niche differentiation caused by high variations in soil environments and plant communities. Both abiotic and biotic factors (e.g. soil pH and bacterial community composition) shaped bacterial networks. However, biotic factors played more important roles than the measured abiotic factors for fungal network assembly. Further analyses suggest that multiple mechanisms including niche overlap/differentiation, cross-feeding and competition between microorganisms could play important roles in shaping soil microbial networks. This study reveals microbial co-occurrence networks in response to different ecological factors, which provides important insights into our comprehensive understanding of microbial network assembly and their functional potentials in mountain ecosystems.

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient.

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone.

Ecotones between distinct ecosystems have been the focus of many studies as they offer valuable insights into key drivers of community structure and ecological processes that underpin function. While previous studies have examined a wide range of above‐ground parameters in ecotones, soil microbial communities have received little attention. Here we investigated spatial patterns, composition, and co‐occurrences of archaea, bacteria, and fungi, and their relationships with soil ecological processes across a woodland‐grassland ecotone. Geostatistical kriging and network analysis revealed that the community structure and spatial patterns of soil microbiota varied considerably between three habitat components across the ecotone. Woodland samples had significantly higher diversity of archaea while the grassland samples had significantly higher diversity of bacteria. Microbial co‐occurrences reflected differences in soil properties and ecological processes. While microbial networks were dominated by bacterial nodes, different ecological processes were linked to specific microbial guilds. For example, soil phosphorus and phosphatase activity formed the largest clusters in their respective networks, and two lignolytic enzymes formed joined clusters. Bacterial ammonia oxidizers were dominant over archaeal oxidizers and showed a significant association (p < 0.001) with potential nitrification (PNR), with the PNR subnetwork being dominated by Betaproteobacteria. The top ten keystone taxa comprised six bacterial and four fungal OTUs, with Random Forest Analysis revealing soil carbon and nitrogen as the determinants of the abundance of keystone taxa. Our results highlight the importance of assessing interkingdom associations in soil microbial networks. Overall, this study shows how ecotones can be used as a model to delineate microbial structural patterns and ecological processes across adjoining land‐uses within a landscape.

Integrated network analysis reveals the importance of microbial interactions for maize growth.

Microbes play a critical role in soil global biogeochemical circulation and microbe-microbe interactions have also evoked enormous interests in recent years. Utilization of green manures can stimulate microbial activity and affect microbial composition and diversity. However, few studies focus on the microbial interactions or detect the key functional members in communities. With the advances of metagenomic technologies, network analysis has been used as a powerful tool to detect robust interactions between microbial members. Here, random matrix theory-based network analysis was used to investigate the microbial networks in response to four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) over two growth cycles from October 2012 to September 2014. The results showed that the topological properties of microbial networks were dramatically altered by green manure fertilization. Microbial network under milk vetch amendment showed substantially more intense complexity and interactions than other fertilization systems, indicating that milk vetch provided a favorable condition for microbial interactions and niche sharing. The shift of microbial interactions could be attributed to the changes in some major soil traits and the interactions might be correlated to plant growth and production. With the stimuli of green manures, positive interactions predominated the network eventually and the network complexity was in consistency with maize productivity, which suggested that the complex soil microbial networks might benefit to plants rather than simple ones, because complex networks would hold strong the ability to cope with environment changes or suppress soil-borne pathogen infection on plants. In addition, network analyses discerned some putative keystone taxa and seven of them had directly positive interactions with maize yield, which suggested their important roles in maintaining environmental functions and in improving plant growth.

Soil protist communities form a dynamic hub in the soil microbiome.

Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions.

Cross-biome comparison of microbial association networks.

Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a sufficiently large sample number, these microbial communities can be explored by constructing and analyzing co-occurrence networks, which detect taxon associations from abundance data and can give insights into community structure. Here, we investigate how co-occurrence networks differ across biomes and which other factors influence their properties. For this, we inferred microbial association networks from 20 different 16S rDNA sequencing data sets and observed that soil microbial networks harbor proportionally fewer positive associations and are less densely interconnected than host-associated networks. After excluding sample number, sequencing depth and beta-diversity as possible drivers, we found a negative correlation between community evenness and positive edge percentage. This correlation likely results from a skewed distribution of negative interactions, which take place preferentially between less prevalent taxa. Overall, our results suggest an under-appreciated role of evenness in shaping microbial association networks.