Living in a fungal world: impact of fungi on soil bacterial niche development

Differential Responses of Soil Bacterial and Fungal Community to Short-Term Crop Tree Management in a Larix gmelinii Plantation

Crop tree management (CTM) is a widely applicable silviculture technology that is used to improve the performance of individual trees. However, only little information is available about the effects of the CTM regime on the soil microbial community structure. We conducted a study to explore the effects of short-term (five years) CTM on the soil bacterial and fungal diversity, community composition, and structure in the 0–10 cm soil layer in a Larix gmelinii (Rupr.) Kuzen. plantation. We set out to investigate the differential response of bacterial and fungal communities to variations in soil properties mediated by short-term CTM. Compared with the control plots, the soil microbial biomass carbon and microbial biomass nitrogen in CTM increased significantly by 64.2% and 32.3%, respectively. CTM significantly promoted the content of soil organic carbon, dissolved organic carbon, and nitrate nitrogen, and reduced the content of dissolved organic nitrogen. CTM changed the Shannon and Simpson indices of soil fungi to a remarkable extent but had little effect on the α diversity of bacterial communities. The bacterial β diversity was more sensitive to CTM than fungi. The relative abundance of Verrucomicrobiae (the dominant class of soil bacteria) in CTM was significantly increased by 78.2%, while the relative abundance of Agaricomycetes (dominant class for soil fungi) was reduced by 43.3%. We observed a significantly increased number of unique OTUs for soil fungi in the CTM plots. Redundancy analysis showed that dissolved organic carbon, soil moisture, and total phosphorus content significantly affected the composition of bacterial communities, while soil dissolved organic nitrogen, C/N, and total phosphorus drove the high variation in fungal community composition. Overall, our results emphasize the divergent response of soil bacterial and fungal communities in Larix gmelinii plantations to short-term CTM. We must pay more attention to the functional role of soil microbiota in future forest management.

Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation

Soil organic matter is composed of a variety of carbon (C) forms. However, not all forms are equally accessible to soil microorganisms. Deprivation of C inputs will cause changes in the physical and microbial community structures of soils; yet the trajectories of such changes are not clear. We assessed microbial communities using phospholipid fatty acid profiling, metabarcoding, CO₂ emissions, and functional gene microarrays in a decade-long C deprivation field experiment. We also assessed changes in a range of soil physicochemical properties, including using X-ray Computed Tomography imaging to assess differences in soil structure. Two sets of soils were deprived of C inputs by removing plant inputs for 10 years and 1 year, respectively. We found a reduction in diversity measures, after 10 years of C deprivation, which was unexpected based on previous research. Fungi appeared to be most impacted, likely due to competition for scarce resources after exhausting the available plant material. This suggestion was supported by evidence of bioindicator taxa in non-vegetated soils that may directly compete with or consume fungi. There was also a reduction in copies of most functional genes after 10 years of C deprivation, though gene copies increased for phytase and some genes involved in decomposing recalcitrant C and methanogenesis. Additionally, soils under C deprivation displayed expected reductions in pH, organic C, nitrogen, and biomass as well as reduced mean pore size, especially in larger pores. However, pore connectivity increased after 10 years of C deprivation contrary to expectations. Our results highlight concurrent collapse of soil structure and biodiversity following long-term C deprivation. Overall, this study shows the negative trajectory of continuous C deprivation and loss of organic matter on a wide range of soil quality indicators and microorganisms.

The Response of Critical Microbial Taxa to Litter Micro-Nutrients and Macro-Chemistry Determined the Agricultural Soil Priming Intensity After Afforestation

Afforestation with trees and shrubs around cropland can effectively decrease soil degradation and avoid sand storms, but subsequent modification of litter quality accelerates the degradation of native organic matter via the soil priming effect (PE). Although carbon accumulation in agricultural soils after afforestation was widely studied, little is known about the extent to which soil organic carbon (SOC) mineralization is induced by complex residue input in agro-forest-grass composite ecosystems. Here, we mixed corn field soil and litter of afforestation tree and shrub species together in a micro-environment to quantify the effects of litter-mixture input on farmland soil priming associated with afforestation. Additionally, we studied the responses of bacterial and fungal species to litter chemistry, with the aim to identify the litter and microbial driver of soil priming. The results showed that soil priming was accelerated by different litter addition which varied from 24 to 74% of SOC mineralization, suggesting that priming intensity was relatively flexible and highly affected by litter quality. We also find that the macro-chemistry (including litter carbon, nitrogen, lignin, and cellulose) directly affects priming intensity, while micro-chemistry (including litter soluble sugar, water-soluble phenol, methanol-soluble phenol, and condensed tannin) indirectly influences priming via alteration to dominant bacterial taxa. The stepwise regression analysis suggested that litter nitrogen and cellulose were the critical litter drivers to soil priming (r 2 = 0.279), and the combination of bacterial phylum Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and fungal taxa Eurotiomycetes was a great model to explain the priming intensity (r 2 = 0.407).

Disease-induced changes in plant microbiome assembly and functional adaptation

BACKGROUND

The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.

RESULTS

The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants.

CONCLUSIONS

Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

Insights into the Role of the Fungal Community in Variations of the Antibiotic Resistome in the Soil Collembolan Gut Microbiome

Fertilization is known to affect antibiotic-resistance gene (ARG) patterns in the soil, even in the gut of soil fauna. Here, we conducted a microcosm experiment to investigate differences of effects of different fertilizers on collembolan gut ARG profiles and to further explore the microecological mechanisms that cause the differences. Although fertilization increased the abundance of ARGs, compared with the conventional manure, the application of antibiotic-reduced manure and vermicompost all curbed the enrichment of ARGs in the gut of collembolans. The results of the structural equation model revealed that changes in the microbial community caused by fertilizations have an important contribution to variations in the ARGs. We further found that the fungal community, like bacterial community, is also an important driver of ARG patterns in the collembolan gut. The fungi belonging to Dokmaia and Talaromyces were significantly correlated with the ARGs in the gut of collembolans. In addition, the application of vermicompost significantly increased the abundance of agricultural beneficial microbes in the soil environment. Together, our results provide an insight into the role of the fungal community on ARG patterns in the soil collembolan gut microbiome and highlight environmental friendliness of vermicomposting.

Community composition of aquatic fungi across the thawing Arctic

Thermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.

Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant

Understanding the ecological patterns of rhizosphere microbial communities is critical for propelling sustainable agriculture and managing ecosystem functions by exploiting microorganisms. However, this knowledge is still unclear, especially under host-associated large-scale and regarding the comparison between bacteria and fungi. We examined community assembly processes and community characters including environmental thresholds and co-occurrence patterns across the cultivatable area of Panax notoginseng for bacteria and fungi. Both are vital members of the rhizosphere but differ considerably in their life history and dispersal potentiality. Edaphic factors drove the parallel variations of bacterial and fungal communities. Although bacterial and fungal communities exhibited similar biogeographic patterns, the assembly of fungi was more driven by dispersal limitation than selection compared with bacteria. This finding supported the 'size-dispersal' hypothesis. pH and total nitrogen respectively mediated the relative importance of deterministic and stochastic processes in shaping bacterial and fungal communities. In addition, fungal communities exhibited potentially broader environmental thresholds and more modular co-occurrence patterns than bacteria (bacteria: 0.67; fungi: 0.78). These results emphasized the importance of dispersal limitation in structuring rhizosphere microbiota and shaping community features of ecologically distinct microorganisms. This study provides insights into the improved prediction and management of the key functions of rhizosphere microbiota.

Divergent vertical distributions of microbial biomass with soil depth among groups and land uses

Soil microbial biomass is key to improving the prediction of soil organic carbon (SOC) dynamics by modeling. However, the driving mechanism of microbial biomass of different groups with soil depth is poorly understood across sites. Here, we compiled the biomass of different microbial groups (i.e., fungi, bacteria, gram-positive bacteria G⁺, and gram-negative bacteria G^-) from the surface to a soil depth of 1 m from 71 soil profiles across three continents. We found that the biomass of microbial groups all decreased with soil depth but at different magnitudes, while the relative abundance of microbial groups, except G^-, was relatively stable along soil profiles. Soil fungal biomass had a shallower vertical distribution than bacteria, especially G⁺, with 89% fungi and 76% G⁺ in the top 10 cm soils. In addition, a greater proportion of microbial biomass (71-89%) compared to SOC (64%) was in the top 10 cm soils, suggesting that microbes and SOC exhibited different vertical distributions. The vertical distributions of microbial biomass of different groups were significantly correlated with SOC and clay content but not with climate, and these distributions were different among land uses, highlighting the great influences of edaphic factors on vertical distributions of microbial biomass. The relationship between microbial biomass and soil depth provides a feasible way to estimate microbial biomass at different soil depths, which can serve as a benchmark to improve the prediction of SOC dynamics of entire soil profile at large scales.

Fungal Biodiversity Mediates the Effects of Drying on Freshwater Ecosystem Functioning

Investigating the influence of biodiversity on ecosystem functioning over environmental gradients is needed to anticipate ecosystem responses to global change. However, our understanding of the functional role of freshwater biodiversity, especially for microbes, is mainly based on manipulative experiments, where biodiversity and environmental variability are minimized. Here, we combined observational and manipulative experiments to analyse how fungal biodiversity responds to and mediates the impacts of drying on two key ecosystem processes: organic matter decomposition and fungal biomass accrual. Our observational data set consists of fungal biodiversity and ecosystem processes from 15 streams spanning a natural gradient of flow intermittence. Our manipulative design evaluates the responses of ecosystem processes to two fungal richness levels crossed with three levels of drying. For the observational experiment, we found that increasing the duration of drying reduced fungal species richness and caused compositional changes. Changes in species composition were driven by species turnover, suggesting resistance mechanisms to cope with drying. We also found that fungal richness had a positive effect on organic matter decomposition and fungal biomass accrual. Positive effects of fungal biodiversity were consistent when controlling for the effects of drying duration on richness by means of structural equation modelling. In addition, our results for the manipulative experiment showed that the positive effects of higher richness on both ecosystem processes were evident even when exposed to short or long simulated drying. Overall, our study suggests that maintaining high levels of biodiversity is crucial for maintaining functional freshwater ecosystems in response to ongoing and future environmental changes.

Potential use of fungal-bacterial co-cultures for the removal of organic pollutants

Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.

It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator

Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.

Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.

Particulate organic matter as a functional soil component for persistent soil organic carbon

The largest terrestrial organic carbon pool, carbon in soils, is regulated by an intricate connection between plant carbon inputs, microbial activity, and the soil matrix. This is manifested by how microorganisms, the key players in transforming plant-derived carbon into soil organic carbon, are controlled by the physical arrangement of organic and inorganic soil particles. Here we conduct an incubation of isotopically labelled litter to study effects of soil structure on the fate of litter-derived organic matter. While microbial activity and fungal growth is enhanced in the coarser-textured soil, we show that occlusion of organic matter into aggregates and formation of organo-mineral associations occur concurrently on fresh litter surfaces regardless of soil structure. These two mechanisms—the two most prominent processes contributing to the persistence of organic matter—occur directly at plant–soil interfaces, where surfaces of litter constitute a nucleus in the build-up of soil carbon persistence. We extend the notion of plant litter, i.e., particulate organic matter, from solely an easily available and labile carbon substrate, to a functional component at which persistence of soil carbon is directly determined.

The fate of soil carbon is controlled by plant inputs, microbial activity, and the soil matrix. Here the authors extend the notion of plant-derived particulate organic matter, from an easily available and labile carbon substrate, to a functional component at which persistence of soil carbon is determined.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832^T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836^T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837^T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of strain AVO110.

Attributes of Drying Define the Structure and Functioning of Microbial Communities in Temperate Riverbed Sediment

Combined effects of climate change and increasing anthropogenic water demand have increased and extended dry period occurrences in rivers worldwide. Riverbed drying can significantly affect sediment microorganisms, crucial drivers of biogeochemical processes in lotic systems. In this study, we evaluated how sediment bacterial and fungal community structure and composition (based on 16S rRNA gene and ITS metabarcoding) and microbial functions (community respiration and extracellular enzymatic activities) respond to different riverbed drying intensities over 90 days. Riverbed sediment collected in a flowing reach of the Spree river in northeastern Germany was dried under different rates in outdoor mesocosms during the summer months of 2018. Our results demonstrate that drying attributes (duration and intensity) and sediment organic matter (OM) content play a crucial role in sediment microbial community assembly and functioning throughout drying. Milder drying surprisingly triggered a more rapid and drastic change in the microbial community composition and diversity. After 90 days of drying, Bacilli (Firmicutes) became the dominant bacterial class in most treatments, except in sediments with low OM content under the most severe drying treatment. Fungal amplicon sequence variants (ASVs) from Dothideomycetes (Ascomycota) had by far the highest relative abundance in all our treatments at the end of the drying experiment, making up 65.1% to 94.0% of the fungal reads. CO₂ fluxes, a proxy for sediment community respiration, were rapidly and strongly affected by drying in all treatments. Our results imply that even short riverbed drying periods are likely to have significant consequences for the biogeochemical dynamics in recently formed non-perennial temperate rivers.

Trichoderma-Based Biopreparation with Prebiotics Supplementation for the Naturalization of Raspberry Plant Rhizosphere

The number of raspberry plants dying from a sudden outbreak of gray mold, verticillium wilt, anthracnosis, and phytophthora infection has increased in recent times, leading to crop failure. The plants suffer tissue collapse and black roots, symptoms similar to a Botrytis-Verticillium-Colletotrichum-Phytophthora disease complex. A sizeable number of fungal isolates were acquired from the root and rhizosphere samples of wild raspberries from different locations. Subsequent in vitro tests revealed that a core consortium of 11 isolates of selected Trichoderma spp. was the most essential element for reducing in phytopathogen expansion. For this purpose, isolates were characterized by the efficiency of their antagonistic properties against Botrytis, Verticillium, Colletotrichum and Phytophthora isolates and with hydrolytic properties accelerating the decomposition of organic matter in the soil and thus making nutrients available to plants. Prebiotic additive supplementation with a mixture of adonitol, arabitol, erythritol, mannitol, sorbitol, and adenosine was proven in a laboratory experiment to be efficient in stimulating the growth of Trichoderma isolates. Through an in vivo pathosystem experiment, different raspberry naturalization-protection strategies (root inoculations and watering with native Trichoderma isolates, applied separately or simultaneously) were tested under controlled phytotron conditions. The experimental application of phytopathogens attenuated raspberry plant and soil properties, while Trichoderma consortium incorporation exhibited a certain trend of improving these features in terms of a short-term response, depending on the pathosystem and naturalization strategy. What is more, a laboratory-scale development of a biopreparation for the naturalization of the raspberry rhizosphere based on the Trichoderma consortium was proposed in the context of two application scenarios. The first was a ready-to-use formulation to be introduced while planting (pellets, gel). The second was a variant to be applied with naturalizing watering (soluble powder).

Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.

Friends or Foes-Microbial Interactions in Nature

Simple Summary

Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability.

Abstract

Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.

Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics

Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber’s appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.

A Seed Mucilage-Degrading Fungus From the Rhizosphere Strengthens the Plant-Soil-Microbe Continuum and Potentially Regulates Root Nutrients of a Cold Desert Shrub

Seed mucilage plays important roles in the adaptation of desert plants to the stressful environment. Artemisia sphaerocephala is an important pioneer plant in the Central Asian cold desert, and it produces a large quantity of seed mucilage. Seed mucilage of A. sphaerocephala can be degraded by soil microbes, but it is unknown which microorganisms can degrade mucilage or how the mucilage-degrading microorganisms affect rhizosphere microbial communities or root nutrients. Here, mucilage-degrading microorganisms were isolated from the rhizosphere of A. sphaerocephala, were screened by incubation with mucilage stained with Congo red, and were identified by sequencing and phylogenetic analyses. Fungal-bacterial networks based on high-throughput sequencing of rhizosphere microbes were constructed to explore the seasonal dynamic of interactions between a mucilage-degrading microorganism and its closely related microorganisms. The structural equation model was used to analyze effects of the mucilage-degrading microorganism, rhizosphere fungal-bacterial communities, and soil physicochemical properties on root C and N. The fungus Phanerochaete chrysosporium was identified as a mucilage-degrading microorganism. Relative abundance of the mucilage-degrading fungus (MDF) was highest in May. Subnetworks showed that the abundance of fungi and bacteria closely related to the MDF also were highest in May. Interactions between the MDF and related fungi and bacteria were positive, which might enhance mucilage degradation. In addition, the MDF might regulate root C and N by affecting rhizosphere microbial community structure. Our results suggest that MDF from the rhizosphere strengthens the plant-soil-microbe continuum, thereby potentially regulating microbial interactions and root nutrients of A. sphaerocephala.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The Responses to Long-Term Water Addition of Soil Bacterial, Archaeal, and Fungal Communities in A Desert Ecosystem

The response of microbial communities to continual and prolonged water exposure provides useful insight when facing global climate changes that cause increased and uneven precipitation and extreme rainfall events. In this study, we investigated an in situ manipulative experiment with four levels of water exposure (ambient precipitation +0%, +25%, +50%, and +100% of local annual mean precipitation) in a desert ecosystem of China. After 9 years of water addition, Illumina sequencing was used to analyze taxonomic compositions of the soil bacterial, archaeal, and fungal communities. The results showed significant increases in microbial biomass carbon (MBC) at higher amended precipitation levels, with the highest values reported at 100% precipitation. Furthermore, an increase in the bacterial species richness was observed along the water addition gradient. In addition, the relative abundance of several bacterial phyla, such as Proteobacteria, significantly increased, whereas that of some drought-tolerant taxa, including Actinobacteria, Firmicutes, and Bacteroidetes, decreased. In addition, the phyla Planctomycetes and Nitrospirae, associated with nitrification, positively responded to increased precipitation. Archaeal diversity significantly reduced under 100% treatment, with changes in the relative abundance of Thaumarchaeota and Euryarchaeota being the main contributors to shifts in the archaeal community. The fungal community composition was stable in response to water addition. Results from the Mantel test and structural equation models suggested that bacterial and archaeal communities reacted contrastingly to water addition. Bacterial community composition was directly affected by changing soil moisture and temperature, while archaeal community composition was indirectly affected by changing nitrogen availability. These findings highlight the importance of soil moisture and nitrogen in driving microbial responses to long-term precipitation changes in the desert ecosystem.

Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans

The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.

The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes

Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.

Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches

Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.

Biotic and abiotic factors distinctly drive contrasting biogeographic patterns between phyllosphere and soil resistomes in natural ecosystems

The phyllosphere and soil are two of the most important reservoirs of antibiotic resistance genes (ARGs) in terrestrial ecosystems. However, comparative studies on the biogeographic patterns of ARGs in these two habitats are lacking. Based on the construction of ARG abundance atlas across a > 4,000 km transect in eastern and northern Australia, we found contrasting biogeographic patterns of the phyllosphere and soil resistomes, which showed their distinct responses to the biotic and abiotic stresses. The similarity of ARG compositions in soil, but not in the phyllosphere, exhibited significant distance-decay patterns. ARG abundance in the phyllosphere was mainly correlated with the compositions of co-occurring bacterial, fungal and protistan communities, indicating that biotic stresses were the main drivers shaping the phyllosphere resistome. Soil ARG abundance was mainly associated with abiotic factors including mean annual temperature and precipitation as well as soil total carbon and nitrogen. Our findings demonstrated the distinct roles of biotic and abiotic factors in shaping resistomes in different environmental habitats. These findings constitute a major advance in our understanding of the current environmental resistomes and contribute to better predictions of the evolution of environmental ARGs by highlighting the importance of habitat difference in shaping environmental resistomes.

Spatial factors and plant attributes influence soil fungal community distribution patterns in the lower reaches of the Heihe River Basin, Northwest China

Inland river basins include critical habitats and provide various ecosystem services in extremely arid lands. However, we know little about the distribution patterns of soil fungal communities in these river basins. We investigated the distribution patterns of soil fungal communities from the riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of the Heihe River. The results indicated that soil fungal communities were mainly dominated by the phyla Ascomycota and Basidiomycota across all samples. The dominant soil fungi taxa were significantly different between ROZ and CDZ habitats at both the phylum and genus levels. Fungal alpha diversity was mainly affected by spatial factors and plant functional traits, and Pearson correlation analysis revealed that fungal alpha diversity was more closely related to plant functional traits than soil properties. Furthermore, fungal community structure was best explained by spatial factors and plant attributes (including plant diversity and plant functional traits). Together, our findings provide new insights into the significance of spatial factors and plant attributes for predicting distributions of fungal communities in arid inland river basins, which will help us better understand the functions and services of these ecosystems.

Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling

Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity-MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function.IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.

Veteran trees have divergent effects on beetle diversity and wood decomposition

Veteran hollow trees are keystone structures in ecosystems and provide important habitat for a diverse set of organisms, many of which are involved in the process of decomposition. Since veteran trees are 'islands' of high biodiversity, they provide a unique system in which to study the relationship between biodiversity and decomposition of wood. We tested this relationship with a balanced experiential design, where we quantified the taxonomic and functional diversity of beetles directly involved in the process of decomposing wood, and measured the decomposition of experimentally added bundles of small diameter wood around 20 veteran trees and 20 nearby young trees in southern Norway. We found that the diversity (both taxonomic and functional) of wood-decomposing beetles was significantly higher around the veteran trees, and beetle communities around veteran trees consisted of species with a greater preference for larger diameter wood. We extracted few beetles from the experimentally added wood bundles, regardless of the tree type that they were placed near, but decomposition rates were significantly lower around veteran trees. We speculate that slower decomposition rates around veteran trees could have been a result of a greater diversity of competing fungi, which has been found to decrease decay rates. Veteran trees provide an ecological legacy within anthropogenic landscapes, enhance biodiversity and influence wood decomposition. Actions to protect veteran trees are urgently needed in order to save these valuable organisms and their associated biodiversity.

Spatial patterns and co-occurrence networks of microbial communities related to environmental heterogeneity in deep-sea surface sediments around Yap Trench, Western Pacific Ocean

Microbial communities are a large component of abyssal and hadal benthic environments, especially in deep-sea areas like Yap Trench, they provide a continuous source of nutrients and energy in their unique ecosystems. However, due to sampling difficulties, these microbial communities are relatively understudied. In the summer of 2017, sediment samples were collected from 21 stations around Yap Trench in the Western Pacific Ocean (mostly in the West Caroline Basin), at depths ranging from 3156 to 7837 m. Sediment samples from deep water depths and shallow water depths differed in organic matter content, median grain size, silt-clay content, and biodiversity. The structure of the microbial communities in the surface sediments had distinct relationships with environmental factors and their co-occurrence networks exhibited a clear spatial pattern. In addition, for both prokaryotes or eukaryotes, a combination of variables including silt-clay content, organic matter content, median grain size, and depth had the greatest impact on community structure. It was notable that fungi played important roles in the co-occurrence networks of deep water depth sediment samples while bacteria dominated those of shallow water depth samples. The differences in structure and ecological niches in the different networks were due to differences in sediment texture and organic matter content. Since clay had a positive effect on the diversity of bacteria, it had an indirect positive effect on fungi, leading to differences in biodiversity among different groups. More organic matter meant more nutrients were available for the growth and reproduction of microbes, which led to fewer niche overlaps. This study conducted an extensive and systematic sequencing survey of surface sediments around Yap Trench in the Western Pacific Ocean, providing insight into microbial responses to environmental heterogeneity in deep-sea benthic ecosystems.

Polyester microfiber and natural organic matter impact microbial communities, carbon-degraded enzymes, and carbon accumulation in a clayey soil

Microplastics can alter microbial communities and enzymatic activities in soils. However, the influences of microplastics on soil carbon cycling which driven by microbial communities remain largely unknown. In this study, we investigated the effects of polyester microfiber (PMF) and natural organic matter（OM）on soil microbial communities, carbon-degraded enzymes, and carbon accumulation through an incubation experiment. Our results showed that the addition of PMF increased the activities of soil cellulase and laccase but did not impact soil bacterial and fungal communities too much. However, the addition of OM largely altered soil microbial communities and the activities of carbon-degraded enzymes, then mitigated the PMF effects on the activities of soil cellulase and laccase. On the other hand, greater alpha diversity of bacterial community attached on PMF was observed than those in the surrounding soils. The interaction of PMF and OM increased the richness of bacterial community in soils and on PMF. More importantly, we observed that the accumulation of natural organic carbon in soils reduced with increasing PMF. Thus, our results provide valuable insights into the effects of microplastics on soil organic carbon dynamics and microbial communities, and further work is required to clarify the biochemical processes at the surface of microplastics.

Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world

Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.

Production of antimicrobial metabolites against pathogenic bacteria and yeasts by Fusarium oxysporum in submerged culture processes

The antimicrobial activity of the metabolites produced by Fusarium oxysporum PR-33 in submerged culture was evaluated against Gram-positive and Gram-negative bacteria and yeasts. Metabolites were determined by HPLC-DAD-MS/MS. An extract was obtained following the removal of mycelium by centrifugation and lyophilisation of the supernatant. The compounds in this extract demonstrated broad-spectrum antimicrobial action, with rates of inhibition between 60 and 80%, depending on the species and extract tested. The major compounds of the extracts were identified as fusarinolic acid and its isomer [56.9% flask extract (FE)] and 59.2% bioreactor extract (BE), dehydrofusaric acid (35.7% FE and 31.6% BE), and fusaric acid (6.5% FE and 1.1% BE). Fusaric acid has been shown to be responsible for antimicrobial activity. The cytotoxicity of the extracts was evaluated in culture of HEK-293 and SH-SY5Y animal cells and toxicity of these extracts was verified even in the lowest tested concentrations. Therefore, our results indicate that the compounds identified exhibit potential as antimicrobial agents.

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.

Extraordinary Multi-Organismal Interactions Involving Bacteriophages, Bacteria, Fungi, and Rotifers: Quadruple Microbial Trophic Network in Water Droplets

Our observations of predatory fungi trapping rotifers in activated sludge and laboratory culture allowed us to discover a complicated trophic network that includes predatory fungi armed with bacteria and bacteriophages and the rotifers they prey on. Such a network seems to be common in various habitats, although it remains mostly unknown due to its microscopic size. In this study, we isolated and identified fungi and bacteria from activated sludge. We also noticed abundant, virus-like particles in the environment. The fungus developed absorptive hyphae within the prey. The bacteria showed the ability to enter and exit from the hyphae (e.g., from the traps into the caught prey). Our observations indicate that the bacteria and the fungus share nutrients obtained from the rotifer. To narrow the range of bacterial strains isolated from the mycelium, the effects of bacteria supernatants and lysed bacteria were studied. Bacteria isolated from the fungus were capable of immobilizing the rotifer. The strongest negative effect on rotifer mobility was shown by a mixture of Bacillus sp. and Stenotrophomonas maltophilia. The involvement of bacteriophages in rotifer hunting was demonstrated based on molecular analyses and was discussed. The described case seems to be an extraordinary quadruple microbiological puzzle that has not been described and is still far from being understood.

Arbuscular Mycorrhiza Mediates Efficient Recycling From Soil to Plants of Nitrogen Bound in Chitin

Symbiosis between plants and arbuscular mycorrhizal (AM) fungi, involving great majority of extant plant species including most crops, is heavily implicated in plant mineral nutrition, abiotic and biotic stress tolerance, soil aggregate stabilization, as well as shaping soil microbiomes. The latter is particularly important for efficient recycling from soil to plants of nutrients such as phosphorus and nitrogen (N) bound in organic forms. Chitin is one of the most widespread polysaccharides on Earth, and contains substantial amounts of N (>6% by weight). Chitin is present in insect exoskeletons and cell walls of many fungi, and can be degraded by many prokaryotic as well as eukaryotic microbes normally present in soil. However, the AM fungi seem not to have the ability to directly access N bound in chitin molecules, thus relying on microbes in their hyphosphere to gain access to this nutrient-rich resource in the process referred to as organic N mineralization. Here we show, using data from two pot experiments, both including root-free compartments amended with 15N-labeled chitin, that AM fungi can channel substantial proportions (more than 20%) of N supplied as chitin into their plants hosts within as short as 5 weeks. Further, we show that overall N losses (leaching and/or volatilization), sometimes exceeding 50% of the N supplied to the soil as chitin within several weeks, were significantly lower in mycorrhizal as compared to non-mycorrhizal pots. Surprisingly, the rate of chitin mineralization and its N utilization by the AM fungi was at least as fast as that of green manure (clover biomass), based on direct 15N labeling and tracing. This efficient N recycling from soil to plant, observed in mycorrhizal pots, was not strongly affected by the composition of AM fungal communities or environmental context (glasshouse or outdoors, additional mineral N supply to the plants or not). These results indicate that AM fungi in general can be regarded as a critical and robust soil resource with respect to complex soil processes such as organic N mineralization and recycling. More specific research is warranted into the exact molecular mechanisms and microbial players behind the observed patterns.

Potential complementary functions among bacteria, fungi, and archaea involved in carbon cycle during reversal of desertification

Development of biological soil crusts (BSCs) on bare land is a sign of reversal of desertification, and microbial communities of BSCs are the biogeochemical engineers of desert ecosystems. However, regulation of different microbial groups involved in the carbon (C) cycle is not clear. This study investigated the correlation between bacteria, fungi, and archaea of BSCs involved in the C cycle during reversal of desertification through community abundance analysis by quantitative PCR and functional gene detection using GeoChip 5.0. Among the known C cycle genes found in BSCs, 84.5% of C degradation genes, 95% of C fixation genes, and all of methane oxidation genes were derived from bacteria owing to their highest proportion among the total microbial abundance of BSCs; some recalcitrant C degradation genes were derived from fungi; and other C fixation pathway and methanogenesis genes originated from archaea. The increased abundance of bacteria and fungi and decreased abundance of archaea during reversal of desertification, as well as the difference in C cycle genes of the three microbial groups, indicated the functional complementarity among these microorganisms involved in C cycle. At the early stage of BSC development, archaea, and bacteria provide available C sources by autotrophic CO2 fixation pathway; bacteria play important roles in C degradation, C fixation, and methane oxidation during the entire BSC development process; and fungi mainly degrade lignin at the later stage of BSC development. Thus, cooperation among BSC microflora altered C cycle during reversal of desertification.

Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

Enhanced Carbon Sequestration in Marginal Land Upon Shift towards Perennial C4Miscanthus × giganteus: A Case Study in North-Western Czechia

Bioenergy crops such as Miscanthus × giganteus are foreseeable as an alternative source to replace fossil fuel and reduce greenhouse gas emissions. They are also assessed as an environment-friendly solution for polluted, marginal and low-quality agricultural soils. Several studies had been launched on soil organic carbon sequestration potentials of miscanthus culture along with its impacts on restoring soil functionality, most of which focus on the long-term basis of the plant’s cultivation. Nevertheless, information concerning the short term impacts as well as the situation in Czechia is still scarce. In this context, a field experiment was launched in 2017 in a poor-quality agricultural land in the city of Chomutov (North-Western Czechia) to compare the impacts of the perennial C4 miscanthus with an annual C3 forage crop (wheat) on the soil carbon stocks as well as enhancing its functionality. Results through the 0–30 cm soil profile examination showed that miscanthus plants played a role in improving the studied soil physico-chemical (bulk density and soil organic carbon concentrations) and biological (Phospholipid fatty acids stress indicator, basal respiration and fluorescein diacetate hydrolytic activity) parameters. The naturally occurring δ13C concentrations were used to evaluate the direct plant contribution to the total soil organic carbon (SOC) stocks and revealed considerable miscanthus contribution all over the detected soil layers (1.98 ± 0.21 Mg C. ha−1 yr−1) after only 3 growing seasons. It is thus suggested that the C4 perennial miscanthus possess remarkable prospects for SOC sequestration and restoring degraded lands.

Seasonal Changes in Pinus tabuliformis Root-Associated Fungal Microbiota Drive N and P Cycling in Terrestrial Ecosystem

In terrestrial ecosystems, mycorrhizal roots play a key role in the cycling of soil carbon (C) and other nutrients. The impact of environmental factors on the mycorrhizal fungal community has been well studied; however, the seasonal variations in the root-associated fungal microbiota affected by environmental changes are less clear. To improve the understanding of how environmental factors shape the fungal microbiota in mycorrhizal roots, seasonal changes in Pinus tabuliformis root-associated fungi were investigated. In the present study, the seasonal dynamics of edaphic properties, soil enzymatic activities, root fungal colonization rates, and root-associated fungal microbiota in P. tabuliformis forests were studied across four seasons during a whole year to reveal their correlations with environmental changes. The results indicate that the soil functions, such as the enzymatic activities related to nitrogen (N) and phosphorus (P) degradation, were varied with the seasonal changes in microclimate factors, resulting in a significant fluctuation of edaphic properties. In addition, the ectomycorrhizal fungal colonization rate in the host pine tree roots increased during warm seasons (summer and autumn), while the fungal colonization rate of dark septate endophyte was declined. Moreover, the present study indicates that the fungal biomass increased in both the pine roots and rhizospheric soils during warm seasons, while the fungal species richness and diversity decreased. While the Basidiomycota and Ascomycota were the two dominant phyla in both root and soil fungal communities, the higher relative abundance of Basidiomycota taxa presented in warm seasons. In addition, the fungal microbial network complexity declined under the higher temperature and humidity conditions. The present study illustrates that the varieties in connectivity between the microbial networks and in functional taxa of root-associated fungal microbiota significantly influence the soil ecosystem functions, especially the N and P cycling.

Revealing of Non-Cultivable Bacteria Associated with the Mycelium of Fungi in the Kerosene-Degrading Community Isolated from the Contaminated Jet Fuel

Fuel (especially kerosene) biodamage is a challenge for global industry. In aviation, where kerosene is a widely used type of fuel, its biodeterioration leads to significant damage. Six isolates of micromycetes from the TS-1 aviation kerosene samples were obtained. Their ability to grow on the fuel was studied, and the difference between biodegradation ability was shown. Micromycetes belonged to the Talaromyces, Penicillium, and Aspergillus genera. It was impossible to obtain bacterial isolates associated with their mycelium. However, 16S rRNA metabarcoding and microscopic observations revealed the presence of bacteria in the micromycete isolates. It seems to be that kerosene-degrading fungi were associated with uncultured bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were abundant in the fungal cultures isolated from the TS-1 jet fuel samples. Most genera among these phyla are known as hydrocarbon degraders. Only bacteria-containing micromycete isolates were able to grow on the kerosene. Most likely, kerosene degradation mechanisms are based on synergism of bacteria and fungi.

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates

Studies on the effects of trace elements (TEs) (e.g. Cu, Cd, Zn) on soil microbial communities have provided useful information on the toxicity of TEs to microbes. However, previous studies mainly focused on the effects of TEs on microbial community structure in intact soil, while there are few studies on the impact of TEs on microbial community structure in soil aggregates. In this study, soils previously polluted for 20 years, and now containing low and high TE concentrations derived from, now abandoned, metal smelters were sampled from the surface layer (0-15 cm) of two adjacent Chinese paddy fields. The aim was to determine the effects of TEs on the soil microbial biomass and community structure in different sized soil aggregates. Long-term high TE pollution decreased microbial biomass concentration and species, changed the proportion of bacteria and fungi and decreased the diversity of bacteria in the different sized aggregates. The microbial communities in soil aggregates became clustered with increasing TE concentrations.

Metagenomic assessment of the global diversity and distribution of bacteria and fungi

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.

Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness

Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial-fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial-fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.

Changes in the nitrification-denitrification capacity of pilot-scale partially saturated vertical flow wetlands (with corncob in the free-drainage zone) after two years of operation

This six-month study aimed to evaluate the removal of total nitrogen (TN) in two duplicated partially saturated (PS) vertical flow (VF) wetlands added with corncob in two different heights of the free-drainage zone (FDZ) after two years in operation. Both PS VF wetlands efficiently removed organic matter measured as biochemical oxygen demand (BOD₅) and chemical oxygen demand (COD) as well as total suspended solids (TSS) achieving average mass removal efficiencies of 95.3%, 83.2% and 92.9%, respectively, in system I (SI) and 96.3%, 84.0% and 94.9%, respectively, in system II (SII); with no significant differences (p > 0.05) between the systems. Measurements of oxidation-reduction potential (ORP), dissolved oxygen (DO), pH and electrical conductivity (EC) showed suitable conditions in the saturated zone (SZ) of the systems for denitrification process. TN removal was similar in both systems (p > 0.05) (51.5% and 52.9% in SI and SII), and decreased in 15% with respect to the first year. This decrease was due to the lower denitrification capacity of the FDZ as a result of the reduction in the supply of biodegradable carbon by corncob. Denitrification occurred in the SZ, but not at a sufficient level to increase TN removal. NoveltyFirst, the use of lignocellulosic residues in partially saturated vertical wetlands to promote total nitrogen removal is very recent. Furthermore, to the best of our knowledge, this is the first study evaluating TN removal after two years of operation in this type of wetland. Therefore, this study allows us to better understand the function of these systems, in a relatively long term. Thanks to this study: it is possible to confirm that the main process of TN elimination is through the simultaneous nitrification-denitrification process in the free drainage zone (denitrification in the saturated zone is irrelevant) and that TN elimination decreases due to the reduction in carbon supply from the corn, in this area.

Plant-soil feedback responses of four dryland crop species under greenhouse conditions

Plant-soil feedbacks (PSFs) give a mechanistic understanding on how soil properties established by previous plant species go on to influence the performance of the same or different species in monoculture, intercropping or crop rotation systems. We hypothesized that different dryland crops such as Zea mays L., Helianthus annuus L., Phaseolus vulgaris L., and Glycine max L. (Merr.) will have soil legacies that are related to the crop type. We used a two-phase experiment to test plant performance in soils previously cultivated with the same or different plant species under greenhouse conditions. The positive plant growth for all species in their own soil microbiota suggests that mutualists had a greater impact on plant performance than pathogens. The consistent positive soil-feedback results of P. vulgaris were strongly associated with their own beneficial soil microbiota, meaning that the conditioning phase legacy of mutualists and decomposers were more significant than pathogens under monoculture. Despite successful nodulation in sterilized and inoculated soils, G. max unexpectedly showed neutral and insignificant positive plant feedbacks, respectively. Helianthus annuus was superior to other crop species in creating active carbon stocks and an enzymatically active soil for the next crop. Microbial biomass results suggest that raising fungal relative to bacterial biomass can be achieved by increasing the frequency of H. annuus in rotation sequences. However, more studies are necessary to evaluate whether these elevated ratios promote or depress plant performance under field conditions. This study showed that relative to other dryland crops, H. annuus seems to have the potential of increasing fungal to bacterial ratios, raising legacies in active carbon stocks and soil microbial activity that may be crucial to successional planting in dryland systems.