Role Of Microbial Communities Research Articles

Role of microbial communities and nitrogen sources in suppressing root rot disease during ginseng cultivation

Role of microbial communities and nitrogen sources in suppressing root rot disease during ginseng cultivation

Regulation of soil organic carbon dynamics by microbial communities during reforestation of Chinese fir plantations after clear‐cutting

AbstractReforestation after forest clear‐cutting is an effective measure to increase soil organic carbon (SOC) sequestration; still, the soil C balance under reforestation and the role of microbial communities in that process remain to be determined. Samples of organic (0–2 cm) and mineral (2–10 cm) horizons were collected from the 7‐, 15‐, 20‐, 29‐, and 36‐year‐old forest stands of Chinese fir (Cunninghamia lanceolata) after plantation clear‐cutting in subtropical zone under the condition of phosphorus limitation. Particulate organic carbon (POC), mineral‐associated organic carbon (MAOC), microbial phospholipid fatty acids (PLFAs), and enzymatic activities for C, nitrogen (N), and phosphorus (P) acquisition were analyzed. The lowest contents of POC (10%) and MAOC (13%) in the organic horizon were found in 7‐year‐old stands due to the slow tree regrowth and extensive decomposition of SOC in the first years of forest regrowth. POC (2.0×) and MAOC (0.8×) increases in the organic horizon with forest age were attributed to the stand development and accumulation of above‐ and belowground litter. The organic horizon had a higher POC:MAOC ratio than the mineral (0.7–1.1 vs. 0.2–0.5), indicating lower SOC stability in the first one. The ratio of POC:MAOC increased with the Gram‐positive to Gram‐negative bacteria (G+:G‐) ratio, pointing out that microbial communities developed a specific community structure and substrate utilization strategies of organic matter under plantation restoration. The increase of total PLFAs and the G+:G‐ ratio was closely linked with the microbial C and P limitations, indicating that microorganisms shifted community structure to slow‐growing species and increased their content to cope with the C and P restrictions. In the soils of young plantations, microorganisms were limited by C and P; however, the C limitation was alleviated in the 36‐year‐old plots in the organic horizon due to increased litter input, whereas the P limitation was not. This discrepancy between C and P limitation suppressed the decomposition of litter entering the soil, which was seen in decreased specific activity of C degrading enzymes and led to the accumulation of POC in the organic horizon. Thus, soil C sequestration under reforestation of Chinese fir can be controlled by the amount of litter entering the soil and by metabolic C, N, and P limitations that force microorganisms to shift community structure and change their activity.

Roles of Microbial Community and Keystone Taxa in Rice Productivity under Green Manuring in South China

Green manure (GM)–rice–rice rotation is an important management practice for improving soil fertility and rice productivity. The microbiological mechanisms for the increase in grain yield in GM–rice–rice rotation remain unclear. The responses of soil biodiversity, bacterial and fungal communities, and their interactions in the GM–rice–rice rotation were investigated based on two long-term field experiments in Gaoqiao (GQ) and Nanxian (NX) in Hunan Province, south China. Results showed that rice yields were raised by 11.79% and 15.03% under GM in GQ and NX, respectively. GM promoted Shannon diversity and Pielou’s evenness and changed the community structures of bacteria and fungi. The co-occurrence network analysis found that the percentages of negative edges were higher in GM (40.79% and 44.32% in GQ and NX, respectively) than those in the corresponding winter fallow (34.86% and 29.13% in GQ and NX, respectively) in the combined bacterial–fungal networks, suggesting more stable microbial community under GM. Moreover, GM had higher percentages of bacterial–fungal and fungal–fungal edges than winter fallow, indicating that GM increased the interaction between bacteria and fungi and fungi play more essential roles in affecting soil processes under GM. The keystone taxa in GM were positively linked with C metabolism-related enzymes and soil multifunctionality, and were important in improving soil fertility and rice productivity. We concluded that the fungal community was more sensitive to GM application than the bacterial community and that keystone taxa had important influences on soil properties and rice productivity in the GM–double-rice cropping system, which can effectively support the sustainable development of the paddy field ecosystem in southern China.

Unraveling nitrogen loss in paddy soils: A study of anaerobic nitrogen transformation in response to various irrigation practice

Soil nitrogen (N) transformation processes, encompassing denitrification, anaerobic ammonium oxidation (anammox), and anaerobic ammonium oxidation coupled with iron reduction (Feammox), constitute the primary mechanisms of soil dinitrogen (N2) loss. Despite the significance of these processes, there is a notable gap in research regarding the assessment of managed fertilization and irrigation impacts on anaerobic N transformations in paddy soil, crucial for achieving sustainable soil fertility management. This study addressed the gap by investigating the contributions of soil denitrification, anammox, and Feammox to N2 loss in paddy soil across varying soil depths, employing different fertilization and irrigation practices by utilizing N stable isotope technique for comprehensive insights. The results showed that anaerobic N transformation processes decreased with increasing soil depth under alternate wetting and drying (AWD) irrigation, but increased with the increasing soil depth under conventional continuous flooding (CF) irrigation. The denitrification and anammox rates varied from 0.41 to 2.12 mg N kg−1 d−1 and 0.062–0.394 mg N kg−1 d−1, respectively, which accounted for 84.3–88.1% and 11.8–15.7% of the total soil N2 loss. Significant correlations were found among denitrification rate and anammox rate (r = 0.986, p < 0.01), Fe (Ⅲ) reduction rate and denitrification rate (r = 0.527, p < 0.05), and Fe(Ⅲ) reduction rate and anammox rate (r = 0.622, p < 0.05). Moreover, nitrogen loss was more pronounced in the surface layer of the paddy soil compared to the deep layer. The study revealed that denitrification predominantly contributed to N loss in the surface soil, while Feammox emerged as a significant N loss pathway at depths ranging from 20 to 40 cm, accounting for up to 26.1% of the N loss. It was concluded that fertilization, irrigation, and soil depth significantly influenced anaerobic N transformation processes. In addition, the CF irrigation practice is best option to reduce N loss under managed fertilization. Furthermore, the role of microbial communities and their response to varying soil depths, fertilization practices, and irrigation methods could enhance our understanding on nitrogen loss pathways should be explored in future study.

Strong associations between dissolved organic matter and microbial communities in the sediments of Qinghai-Tibetan Plateau lakes depend on salinity

In aquatic ecosystems, dissolved organic matter (DOM) plays a vital role in microbial communities and the biogeochemical cycling of elements. However, little is known about the associations between DOM and microbial communities in lake sediments. This study investigated the composition of water-extractable organic matter and microbial communities in surface sediments of lakes with different salinities on the Qinghai-Tibet Plateau. Ultrahigh-resolution mass spectrometry and high-throughput microbial sequencing techniques were employed to assess the associations between molecular diversity and microbial diversity and the effects of salinity in 19 lakes spanning a salinity range from 0.22 ‰ to 341.87 ‰. Our results show that increasing salinity of lake water led to higher molecular diversity of DOM in surface sediments. High-salinity lakes exhibited distinct DOM characteristics, such as lower aromaticity, smaller molecular weight, and higher oxidation degree, compared to freshwater lakes. The complexity of the microbial network composition of sediments first increased and then decreased with the increase of salinity. Moreover, as salinity increases, the dominant species transitioned from Gammaproteobacteria to Bacteroidia, and this transition was accompanied by a decrease in microbial diversity and an increase in molecular diversity. Microbial factors accounted for 34.68 % of the variation in the molecular composition of DOM. Overall, this study emphasizes the significant effects of salinity on both molecular and microbial diversity in lake sediments. Furthermore, our findings underscore the importance of microbes in controlling the range of organic compounds present in lakes and deepen our knowledge of the biogeochemical cycling of DOM.

Importance of pathobiomes to the success of microbial weed biocontrol agents

The role of microbial communities in the establishment of plant pathogens introduced to new environments as weed biocontrol agents is relatively unexplored. Substantial evidence from crop protection research shows how bulk microbial communities influence the establishment, survival, and success of pathogens. Just as mismatches between biocontrol agents, host genotypes, and climate can lead to establishment failure, we propose that mismatches between microbial biocontrol agents and resident microbiomes may be a cause of apparent weed biocontrol failures. From this perspective, we discuss recent progress in research on plant-associated microbial communities whose interactions influence disease development, or “pathobiomes,” and consider the implications for biocontrol agent evaluation and release. Open questions about how weed pathobiomes develop and influence agent success rates provide ample opportunity for researchers to adapt new methods and analytical frameworks that will enhance biocontrol programs. We conclude by prioritizing the development of standard methods to include microbiomes as a component of release studies. Developing a pathobiome-aware agent selection and release process will improve agent establishment rates and biocontrol outcomes.

Role of Microbial Communities in Compost and Plant Growth: Structure and Function

The review explores the microbial communities within composite composts, focusing on their role in decomposition and nutrient cycling, using advanced molecular techniques and traditional microbiological assays, the researchers examine the diverse bacteria, fungi, and archaea in compost matrices, they highlight the richness and complexity of these ecosystems, their adaptability to various environmental conditions, and their substrate compositions. Certain important groups of microorganisms are essential for breaking down organic material, releasing nutrients, and creating humic substances that are vital for soil health and plant development. The research also shows how the makeup of the microbial community and the conditions of composting work together, which has a big impact on how well the compost matures and how good the final product is.

A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.

Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for the rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged, including the study of the gut microbiome and its health implications and the role of microbial communities in global ecosystems. However, all the critical steps in this framework, from model construction to simulation, require the use of powerful linear optimization solvers, with the choice often relying on commercial solvers for their well-known computational efficiency. In this work, I benchmark a total of six solvers (two commercial and four open source) and measure their performance to solve linear and mixed-integer linear problems of increasing complexity. Although commercial solvers are still the fastest, at least two open-source solvers show comparable performance. These results show that genome-scale metabolic modeling does not need to be hindered by commercial licensing schemes and can become a truly open science framework for solving urgent societal challenges.IMPORTANCEModeling the metabolism of organisms and communities allows for computational exploration of their metabolic capabilities and testing their response to genetic and environmental perturbations. This holds the potential to address multiple societal issues related to human health and the environment. One of the current limitations is the use of commercial optimization solvers with restrictive licenses for academic and non-academic use. This work compares the performance of several commercial and open-source solvers to solve some of the most complex problems in the field. Benchmarking results show that, although commercial solvers are indeed faster, some of the open-source options can also efficiently tackle the hardest problems, showing great promise for the development of open science applications.

Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition.

The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.

Changes in the soil fungal communities of steppe grasslands at varying degradation levels in North China.

The grasslands in North China are rich in fungal resources. However, the knowledge of the structure and function of fungal communities and the role of microbial communities in vegetation restoration and succession are limited. Thus, we used an Illumina HiSeq PE250 high-throughput sequencing platform to study the changing characteristics of soil fungal communities in degraded grasslands, which were categorized as non-degraded (ND), lightly degraded, moderately degraded, and severely degraded (SD). Moreover, a correlation analysis between soil physical and chemical properties and fungal communities was completed. The results showed that the number of plant species, vegetation coverage, aboveground biomass, and diversity index decreased significantly with increasing degradation, and there were significant differences in the physical and chemical properties of the soil among the different degraded grasslands. The dominant fungal phyla in the degraded grassland were as follows: Ascomycota, 44.88%-65.03%; Basidiomycota, 12.68%-29.91%; and unclassified, 5.51%-16.91%. The dominant fungi were as follows: Mortierella, 6.50%-11.41%; Chaetomium, 6.71%-11.58%; others, 25.95%-36.14%; and unclassified, 25.56%-53.0%. There were significant differences in the microbial Shannon-Wiener and Chao1 indices between the ND and degraded meadows, and the composition and diversity of the soil fungal community differed significantly as the meadows continued to deteriorate. The results showed that pH was the most critical factor affecting soil microbial and fungal communities in SD grasslands, whereas soil microbial and fungal communities in ND grasslands were mainly affected by water content and other environmental factors.

Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.

Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use

ABSTRACT Opioid crisis is an ongoing epidemic since the past several decades in the United States. Opioid use-associated microbial dysbiosis is emerging as a key regulator of intestinal homeostasis and behavioral responses to opioid. However, the mechanistic insight into the role of microbial community in modulating host response is unavailable. To uncover the role of opioid-induced dysbiosis in disrupting intestinal homeostasis we utilized whole genome sequencing, untargeted metabolomics, and mRNA sequencing to identify changes in microbiome, metabolome, and host transcriptome respectively. Morphine treatment resulted in significant expansion of Parasuterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and depletion of Lactobacillus johnsonii. These changes correlated with alterations in lipid metabolites and flavonoids. Significant alteration in microbial metabolism (metabolism of lipids, amino acids, vitamins and cofactors) and increased expression of virulence factors and biosynthesis of lipopolysaccharides (LPS) and lipoteichoic acid (LTA) were observed in microbiome of morphine-treated animals. In concurrence with changes in microbiome and metabolome extensive changes in innate and adaptive immune response, lipid metabolism, and gut barrier dysfunction were observed in the host transcriptome. Microbiome depleted mice displayed lower levels of inflammation, immune response and tissue destruction compared to mice harboring a dysbiotic microbiome in response to morphine treatment, thus establishing dysbiotic microbiome as mediator of morphine gut pathophysiology. Integrative analysis of multi-omics data highlighted the associations between Parasutterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and altered levels of riboflavin, flavonoids, and lipid metabolites including phosphocholines, carnitines, bile acids, and ethanolamines with host gene expression changes involved in inflammation and barrier integrity of intestine. Omic analysis also highlighted the role of probiotic bacteria Lactobacillus johnsonii, metabolites flavonoids and riboflavin that were depleted with morphine as important factors for intestinal homeostasis. This study presents for the first time ever an interactive view of morphine-induced changes in microbial metabolism, strain level gut microbiome analysis and comprehensive view of changes in gut transcriptome. We also identified areas of potential therapeutic interventions to limit microbial dysbiosis and present a unique resource to the opioid research community.

Characterization of acetochlor degradation and role of microbial communities in biofilters with varied substrate types

Northeast China has a large area of cultivated land, and the application of various chemical herbicides is very high. As a high-efficiency herbicide widely used in dry fields, its residue in the environment is also concern. Therefore, low-cost and high efficient control measures are urgently needed. Twelve Biofilter simulation devices were designed to investigate the efficiency and mechanism of removing acetochlor under low-temperature conditions. Biochar (Bio-BF), ceramsite (CER-BF), and gravel (GRA-BF) were chosen to be substrates to compare the effect of substrate type on the removal of acetochlor. The results showed that the biochar (Bio-BF) treatment had the shortest onset time (<1 h), The gravel (GRA-BF) treatment had the longest onset of action (more than 8 h), but the removal effect was essentially the same as the biochar treatment. The 16S rRNA gene sequencing results revealed that different bacterial communities are formed due to different substrates. Proteobacteria and Actinobacteria are the dominant phyla in the three biofilters. Four metabolites, 2-ethyl-6-methyl-N-(ethoxymethyl) acetanilide, N-(2-ethyl-6-methyl phenyl) acetamide, N-(2-ethyl-6-methyl phenyl) formamide, and (2-ethyl-6-methyl phenyl) carbamic acid, were identified using gas phase mass spectrometry. The analysis and prediction of the degradation pathways of acetochlor revealed that Ferribacterium, Klebsiella, and Comamonadaceae belonging to the phylum Proteobacteria and Rhodococcus belonging to the phylum Actinobacteria were the key microorganisms involved in the degradation of acetochlor in the biofilter. Redundancy analysis (RDA) further indicates that dissolved oxygen and temperature are key environmental factors affecting the development of key microbial communities within the biofilter, and that future design of biofilters in Northeast China should focus on how to improve oxygen content and temperature.

Biological Disease Control by Beneficial (Micro)Organisms: Selected Breakthroughs in the Past 50 Years.

Biological control of plant disease by beneficial (micro)organisms is one of the main tools available to preserve plant health within the wider context of One Health and in line with the goals of the Agenda 2030 for Sustainable Development. The commercial development of biocontrol agents, together with a new perspective on the resident microbial community, all supported by innovative "omics" technologies, continues to gain in prominence in plant pathology, addressing the need to feed the increasing world population and to assure safe and secure access to food. The present review considers selected advances within the last 50 years, highlighting those that can be considered as breakthroughs for the biological control research field. Selected examples of successful biocontrol agents and strategies are reported, including the history of the progress in researching Trichoderma isolates as commercial biocontrol agents, the exploitation of mycoviruses to confer hypovirulence to plant pathogenic fungi, the role of microbial communities in the suppressiveness of soils, and evolving approaches including the establishment of synthetic microbial communities.

Extensive Cryptic Diversity and Ecological Associations Uncovered among Mexican and Global Collections of Naegleria and Vermamoeba Species by 18S Ribosomal DNA, Internal Transcribed Spacer, and Cytochrome Oxidase Subunit I Sequence Analysis.

Free-living amoebae (FLA) are phagocytic protists that play crucial roles in microbial communities as significant microbial grazers. However, our current knowledge of their diversity, ecology, and population genetic structures is marginal due to the shallow and biased sampling of ecosystems and the use of few, poorly resolving molecular markers. Thirty-two FLA were isolated from soil and water samples collected across representative ecosystems of the State of Morelos in Central Mexico, including the drinking water distribution system (DWDS) from the state capital. We classified our isolates as members of Acanthamoeba, Vermamoeba, Naegleria, and Tetramitus by 18S ribosomal DNA (rDNA) sequencing. Vermamoeba isolates were recovered exclusively from the DWDS samples. In contrast, Naegleria strains displayed a broad distribution in soil and water samples across the natural ecosystems. We used a combination of phylogenetic and population genetic analyses of internal transcribed spacer (ITS) and cytochrome oxidase subunit I (COI) sequences from our isolates and a comprehensive set of reference sequences to analyze the currently known diversity of Naegleria spp. Significant associations were uncovered between the most prevalent lineages of Naegleria and Vermamoeba and broad ecological and geographical variables at regional and global levels. The population structure and cryptic diversity within the Naegleria galeacystis-Naegleria americana and Vermamoeba vermiformis species complexes were thoroughly analyzed. Our results prove that the genus Vermamoeba, which was previously thought to consist of only one species, actually encompasses at least seven widely distributed species, as indicated by consistent evidence from Bayesian phylogenetics, two species-delimitation programs, and population genetics analyses. IMPORTANCE Our study sheds new light on the population genetic structure of V. vermiformis and diverse Naegleria species. Using improved molecular markers and advanced analytical approaches, we discovered that N. americana, previously considered a single species, actually contains multiple distinct lineages, as revealed by COI sequencing. These lineages are highly differentiated, with little gene flow between them. Our findings demonstrate that the genus Vermamoeba holds multiple cryptic species, requiring a significant taxonomic revision in light of multilocus sequence analyses. These results advance our understanding of the ecology, molecular systematics, and biogeography of these genera and species complexes at both regional and global scales. This study has significant implications for diagnosing amoebal infections and evaluating health risks associated with FLA in domestic and recreational waters.

Metatranscriptomics Reveals Sequential Expression of Genes Involved in the Production of Melanogenesis Inhibitors by the Defined Microbial Species in Fermented Unpolished Black Rice.

Fermented products require metabolic enzymes from the microbial community for desired final products. Using a metatranscriptomic approach, the role of microorganisms in fermented products on producing compounds with a melanogenesis inhibition activity has not yet been reported. Previously, unpolished black rice (UBR) fermented with the E11 starter containing Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Rhizopus oryzae, and Pediococcus pentosaceus (FUBR) showed potent melanogenesis inhibition activity. This study aimed to investigate the function of these defined microbial species in producing melanogenesis inhibitors in the FUBR using a metatranscriptomic approach. The melanogenesis inhibition activity increased in a fermentation time-dependent manner. Genes related to melanogenesis inhibitors synthesis such as carbohydrate metabolism, amino acids synthesis, fatty acids/unsaturated fatty acids synthesis, and carbohydrate transporters were analyzed. Most genes from R. oryzae and P. pentosaceus were upregulated in the early stage of the fermentation process, while those of S. cerevisiae and S. fibuligera were upregulated in the late stage. FUBR production using different combinations of the four microbial species shows that all species were required to produce the highest activity. The FUBR containing at least R. oryzae and/or P. pentosaceus exhibited a certain level of activity. These findings were in agreement with the metatranscriptomic results. Overall, the results suggested that all four species sequentially and/or coordinately synthesized metabolites during the fermentation that led to a FUBR with maximum melanogenesis inhibition activity. This study not only sheds light on crucial functions of certain microbial community on producing the melanogenesis inhibitors, but also paves the way to initiate quality improvement of melanogenesis inhibition activity in the FUBR. IMPORTANCE Fermentation of food is a metabolic process through the action of enzymes from certain microorganisms. Although roles of the microbial community in the fermented food were investigated using metatranscriptomic approach in terms of flavors, but no study has been reported so far on the function of the microorganisms on producing compounds with a melanogenesis inhibition activity. Therefore, this study explained the roles of the defined microorganisms from the selected starter in the fermented unpolished black rice (FUBR) that can produce melanogenesis inhibitor(s) using metatranscriptomic analysis. Genes from different species were upregulated at different fermentation time. All four microbial species in the FUBR sequentially and/or coordinately synthesized metabolites during fermentation that led to a FUBR with maximal melanogenesis inhibition activity. This finding contributes to a deeper understanding of the roles of certain microbial community during fermentation and led to the knowledge-based improvement for the fermented rice with potent melanogenesis inhibition activity.

Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats

BackgroundBiting midges (Culicoides spp.) are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. However, little is known about the role of microbial communities in midge larval habitat utilization in the wild. In this study, we characterized microbial communities (bacterial, protistan, fungal and metazoan) in soils from disturbed (bison and cattle grazed) and undisturbed (non-grazed) pond and spring potential midge larval habitats. We evaluated the influence of habitat and grazing disturbance and their interaction on microbial communities, diversity, presence of midges, and soil properties.ResultsBacterial, protistan, fungal and metazoan community compositions were significantly influenced by habitat and grazing type. Irrespective of habitat and grazing type, soil communities were dominated by phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria (Bacteria); Apicomplexa, Cercozoa, Ciliophora, Ochrophyta (Protists); Chytridiomycota, Cryptomycota (Fungi) and Nematoda, Arthropoda (Metazoa). The relative abundance of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia (Bacteria); Apicomplexa, Lobosa (Protists); Ascomycota, Blastomycotina, Cryptomycota (Fungi); and Platyhelminthes (Metazoa) were significantly affected by grazing type. Of note, midge prevalence was higher in grazed sites (67–100%) than non-grazed (25%). Presence of midges in the soil was negatively correlated with bacterial, protistan, fungal and metazoan beta diversities and metazoan species richness but positively correlated with protistan and fungal species richness. Moreover, total carbon (TC), nitrogen (TN) and organic matter (OM) were negatively correlated with the presence of midges and relative abundances of unclassified Solirubrobacterales (Bacteria) and Chlamydomonadales (Protists) but positively with Proteobacteria and unclassified Burkholderiales (Bacteria).ConclusionsHabitat and grazing type shaped the soil bacterial, protistan, fungal and metazoan communities, their compositions and diversities, as well as presence of midges. Soil properties (TN, TC, OM) also influenced soil microbial communities, diversities and the presence of midges. Prevalence of midges mainly in grazed sites indicates that midges prefer to breed and shelter in a habitat with abundant hosts, probably due to greater accessibility of food (blood meals). These results provide a first glimpse into the microbial communities, soil properties and prevalence of midges in suspected midge larval habitats at a protected natural prairie site.

Acarbose May Function as a Competitive Exclusion Agent for the Producing Bacteria.

Acarbose is a well-known microbial specialized metabolite used clinically to treat type 2 diabetes. This natural pseudo-oligosaccharide (PsOS) shows potent inhibitory activity toward various glycosyl hydrolases, including α-glucosidases and α-amylases. While acarbose and other PsOSs are produced by many different bacteria, their ecological or biological role in microbial communities is still an open question. Here, we show that several PsOS-producing actinobacteria, i.e., Actinoplanes sp. SE50/110 (acarbose producer), Streptomyces glaucescens GLA.O (acarbose producer), and Streptomyces dimorphogenes ATCC 31484 (trestatin producer), can grow in the presence of acarbose, while the growth of the non-PsOS-producing organism Streptomyces coelicolor M1152 was suppressed when starch is the main source of energy. Further investigations using recombinant α-amylases from S. coelicolor M1152 and the PsOS-producing actinobacteria revealed that the S. coelicolor α-amylase was inhibited by acarbose, whereas those from the PsOS-producing bacteria were not inhibited by acarbose. Bioinformatic and protein modeling studies suggested that a point mutation in the α-amylases of the PsOS-producing actinobacteria is responsible for the resistance of those enzymes toward acarbose. Converting the acarbose-resistant α-amylase AcbE to its A304H variant diminished its acarbose-resistance property. Taken together, the results suggest that acarbose is used by the producing bacteria as a competitive exclusion agent to suppress the growth of other microorganisms in their natural environment, while the producing organisms equip themselves with α-amylase variants that are resistant to acarbose.

Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.

Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.

Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi.

An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.