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Western Ghats are designated as world heritage sites and global biodiversity hotspots. Microbial diversity in this forest area has been largely neglected and is getting attention since the end of the last millennium. In this review, we have studied and organized various microorganisms from Western Ghats and their diversity, important characteristics and potential biotechnological applications. Microorganisms from Western Ghats have been explored individually for potential bioactive molecules. While most of the microorganisms were analyzed for antimicrobial activities, there have been studies on microbial promotion of plant growth. The microbes analyzed included from aquatics, soil, rhizosphere, phyllosphere and even as endophytes. There have been microorganisms which have shown antioxidant and anti-cancerous activities. There are microorganisms capable of degrading plant wastes and also xenobiotics. Microorganisms capable of producing industrially important enzymes have also been reported. The present review explores largely neglected microbial diversity with respect to their ability to produce potential bioactive biomolecules.

Interactions between plants and microbiomes play a key role in ecosystem functioning and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, we tested and quantified the effect of different factors driving the diversity and composition of plant-associated microbial communities. We manipulated soil microbial diversity (high or low diversity), plant species ('Solanum tuberosum' or 'S. vernei'), and herbivory (presence or absence of a phloem-feeding insect, 'Macrosiphum euphorbiae') and found that soil microbial diversity influenced the herbivore-associated microbiome composition but also plant species and herbivory influenced the soil microbiome composition. We quantified the relative strength of these effects and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems., Finanziert durch den Open-Access-Publikationsfonds der Westfälischen Wilhelms-Universität Münster (WWU Münster).

Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable., This work was partly funded by the US National Science Foundation, awards #1831582 and #1759831 (to KTK), and by the projects CLG2015_66686-C3-1-P, PGC2018-096956-B-C41 and RTC-2017-6405-1 of the Spanish Ministry of Science, Innovation and Universities (to RRM), which were also supported with European Regional Development Fund (FEDER) funds. RRM acknowledges the financial support of the sabbatical stay at Georgia Tech by the grant PRX18/00048 also from the Spanish Ministry of Science, Innovation and Universities.

The demand for novel and improved medicine from biological sources to cater to the biopharmaceutical sector has increased significantly in recent years. Among the vast and miscellaneous microbial diversity, fungi provide a prolific source of structurally unique and biologically active secondary metabolites. Natural products obtained from fungi have reformed the era of biomedicine, providing effective drugs that have diverse healing potential. In this review, we focus on the isolation, chemical structure, and bioactivity of biomolecules that have been identified and studied for the first time. Further, we also explain in substantial detail that how the vast uninvestigated Emericellopsis and Simplicillium species may serve as a potential treasure trove of chemically diverse compounds.

Chinese rice wine (Huangjiu), a typical representative of traditional fermented foods in China, is distinguished for its unique flavor. Microorganisms play the most important role in the formation of the unique flavor of Huangjiu. The complex flavor components in Huangjiu are closely related to the metabolism of various microorganisms during the traditional brewing. Therefore, understanding the influence of microbiota on the formation of flavor components in Huangjiu is conducive to the production of Huangjiu with high-quality flavor. In recent years, many scholars have conducted a large number of studies on the microbial community and flavor metabolites during the traditional brewing process of Huangjiu, with the help of high-throughput sequencing (HTS) and mass spectrometry-based metabolomics. This review mainly summarized the current study progress of the microbial diversity of fermentation starters (Qu) and brewing process of Huangjiu, and explored the potential relationship between the microbial community and the characteristic flavor formation of Huangjiu. Through the comparative analysis of literatures, we found that Huangjiu has strong regional characteristics due to the differences in raw materials, Qu and traditional brewing techniques. Dynamics of microbial composition during the traditional brewing of Huangjiu in different regions of China are quite different, making Huangjiu in each region have their own flavor characteristics. Therefore, revealing the relationship between brewing microorganisms and flavor characteristics of Huangjiu is helpful to the directional regulation of flavor quality. According to the current research status, it is proposed that in the future, emerging technologies such as multi-omics, artificial intelligence, and machine learning should be applied to further improve the accuracy of the analysis of microbial flora and flavor components in Huangjiu, so as to accurately reveal the relationship between the microbial community and the formation of characteristic flavor of Huangjiu. Afterwards, high-throughput screening of excellent functional strains from the traditional brewing system should be applied to the industrial production of Huangjiu, so as to improve the overall flavor quality and commercial value.

Microbial diversity is essential for the maintenance of the normal structure and function of bioregenerative life support systems (BLSS). As a typical nutrient-deficient environment (NDE), the BLSS does not provide sufficient types of available substrates for microbial communities, and its internal microbial diversity is usually not high due to interspecific competitive exclusion. However, it is reported that microbial diversity is abnormally high in the International Space Station (ISS) after long-term exposure to low-dose ionizing radiation (LDIR). It remains a mystery why LDIR leads to the formation and maintenance of high microbial diversity. In this study, a series of artificial microbial communities have been cultivated in NDE without and with LDIR, respectively. These communities are composed of three common microbial species (Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa) in the ISS. By comparing and analyzing the differences in the microbial physiological and behavioral response characteristics in the two scenarios, a reasonable hypothesis was put forward to elucidate the formation and maintenance mechanisms of high microbial diversity in NDE with LDIR. Then a set of kinetic models were developed based on this hypothesis, observed phenomena, and experimental data. Finally, these kinetic models were sufficiently validated and the hypothesis was fully confirmed through large-scale digital simulations. Briefly, two fundamental succession mechanisms of the microbial communities are supposed to exist in NDE with LDIR: substrate-based negative feedback regulation (SNFR) and microbial delayed responses. These two decisive succession mechanisms can give rise to asynchronously convergent fluctuations of microbial populations and significantly alleviate the interspecific competitions. Such a species-for-quantity strategy drives the microbial communities to form and maintain species diversity with higher richness and evenness. This study can lay the theoretical foundation and provide new ideas for the construction of advanced BLSS featured with more robust structures and stronger function.

Soybean paste was a traditional fermented product in Northeast China, mainly fermented by molds, yeast, Bacillus, and lactic acid bacteria. This study investigated the dynamic changes of the microbial community and biogenic amine content during the fermentation of the traditional soybean paste. The microbial diversity of soybean paste in different regions was analyzed by MiSeq sequencing technology. The results showed that Penicillium and Tetragenococcus were the dominant microorganisms responsible for the fermentation of soybean paste. Biogenic amine was found in the traditional soybean paste at different fermentation stages, putrescine, and tyramine were the mainly biogenic amines and their content increased with the extension of fermentation time. Serratia in the soybean paste was positively correlated with the formation of spermine, cadaverine (p

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.

Rhizosphere microorganisms are the main participants of material transformation and energy cycle in soil. To further explore its composition and variation, the tobacco rhizosphere soil were sequenced by Illumina MiSeq, the microbial community at different growth stages were analyzed and compared. The analysis of Alpha diversity showed that, the Chao1 index, Shannon index of bacteria and Chao1 index of fungi in rhizosphere soil were the highest in tobacco budding stage, while the peak of Shannon index of fungi appeared in tobacco material stage. Principal component analysis (PCA) further showed that at different growth stages, Proteobacteria was the dominant, followed by Actinobacteria, Acidobacteria and Gemmatimonadetes for bacterials; Ascomycota was the dominant, followed by Zygomycota and Basidiomycota for fungi. Under field conditions, the microbial abundance changed with the growth of tobacco, and the microbial diversity reached the peak at budding stage. The bacterial community and abundance between budding and mature stages was highly similar, while the bacterial community in vigorous growth stage is quite different. The similarity of fungal community in budding stage was very low, compared with the other stages; while in other stages was high. This study provides a theoretical basis for further understanding the relationship between tobacco rhizosphere soil microbial diversity and variation, tobacco growth and soil diseases.

BackgroundThe gut microbiome (GM) can influence many biological processes in the host, impacting its health and survival, but the GM can also be influenced by the host’s traits. In vertebrates, Major Histocompatibility Complex (MHC) genes play a pivotal role in combatting pathogens and are thought to shape the host’s GM. Despite this—and the documented importance of both GM and MHC variation to individual fitness—few studies have investigated the association between the GM and MHC in the wild.ResultsWe characterised MHC class I (MHC-I), MHC class II (MHC-II) and GM variation in individuals within a natural population of the Seychelles warbler (Acrocephalus sechellensis). We determined how the diversity and composition of the GM varied with MHC characteristics, in addition to environmental factors and other host traits. Our results show that the presence of specific MHC alleles, but not MHC diversity, influences both the diversity and composition of the GM in this population. MHC-I alleles, rather than MHC-II alleles, had the greatest impact on the GM. GM diversity was negatively associated with the presence of three MHC-I alleles (Ase-ua3, Ase-ua4, Ase-ua5), and one MHC-II allele (Ase-dab4), while changes in GM composition were associated with the presence of four different MHC-I alleles (Ase-ua1, Ase-ua7, Ase-ua10, Ase-ua11). There were no associations between GM diversity andTLR3genotype, but GM diversity was positively correlated with genome-wide heterozygosity and varied with host age and field period.ConclusionsThese results suggest that components of the host’s immune system play a role in shaping the GM of wild animals. Host genotype—specifically MHC-I and to a lesser degree MHC-II variation—can modulate the GM, although whether this occurs directly, or indirectly through effects on host health, is unclear. Importantly, if immune genes can regulate host health through modulation of the microbiome, then it is plausible that the microbiome could also influence selection on immune genes. As such, host–microbiome coevolution may play a role in maintaining functional immunogenetic variation within natural vertebrate populations.

The dysregulation of skin microflora in patients with atopic dermatitis (AD) has become a research hotspot in recent years. Metagenomic studies have shown that microbial diversity is decreased, whereas the Staphylococcus aureus infection is increased in AD. Keratinocytes are the primary barrier against the invasion of external pathogenic microorganisms. Staphylococcus aureus infection can abnormally activate innate and adaptive immune responses in keratinocytes, resulting in a vicious cycle between Staphylococcus aureus infection and AD. This article reviews the mechanisms of inflammatory damage of keratinocytes induced by Staphylococcus aureus infection in patients with AD, providing a theoretical basis for the study of new targeted drugs. This review also suggests for the management of Staphylococcus aureus infection in patients with AD.

Aging induces significant shifts in the composition of gut microbiota associated with decreased microbial diversity. Age-related changes in gut microbiota include a loss of commensals and an increase in disease-associated pathobionts. These alterations are accelerated by lifestyle factors, such as poor nutritional habits, physical inactivity, and medications. Given that diet is one of the main drivers shaping the gut microbiota, nutritional interventions for restoring gut homeostasis are of great importance to the overall health of older adults. Polyphenols, ubiquitously present in fruits and vegetables, have emerged as promising anti-aging candidates because of their ability to modulate some of the common denominators of aging, including gut dysbiosis. These compounds can influence the composition of the gut microbiota, and gut bacteria metabolize polyphenols into bioactive compounds that produce relevant health effects. Although the role of polyphenols on the aging gut has not been fully characterized, accumulating evidence suggests that these compounds exert selective effects on the gut microbial community. Here, we discuss the reciprocal interactions between polyphenols and gut microbiota and summarize the latest findings on the effects of polyphenols on modulating intestinal bacteria during aging.

Fecal microbiota transplantation (FMT) is a highly effective therapeutic procedure for treating recurrent Clostridium difficile infection. However, the effectiveness of the FMT for the treatment of other chronic diseases associated with intestinal dysbiosis, until recently, remained very low and very variable. A number of studies conducted in recent years have suggested that the success of the FMT is largely dependent on the microbial diversity and composition of the donor stool, which has led to the concept of the existence of FMT superdonors, which are considered individuals whose FMT is accompanied by a high efficiency. The review presents some of the results of the FMT with the involvement of superdonors, describes the possible mechanisms and factors affecting the success of the FMT. It is concluded that the high diversity of the gut microbiota, especially in the donor, seems to be the best predictor of the patient’s response to the FMT. It is assumed that the identification and subsequent characterization of superdonor intestinal microbiomes will improve our understanding of the microbial component of chronic diseases and will allow the use of the FMT in a more targeted manner in the future.

Global temperatures are steadily increasing, leading to significant changes in microbial diversity and ecology. In the present study, we isolated high-temperature-growing fungi and fungi-like group (Oomycota) strains from freshwater environments of Korea and identified them based on cultural, morphological, and multilocus phylogenetic analyses. As a result, we introduce Saksenaea (Fungi) isolates as a new species, Saksenaea longicolla sp. nov. and record Phytophthora chlamydospora and P. lagoariana (Oomycota) new to Korea. In the growth experiments, they exhibited high-temperature tolerance, which can grow at 35–40 °C but become inactive at 4 °C and below. This study confirms the presence of high-temperature-tolerant fungi and oomycetes in Korea and suggests that the Korean climate conditions are changing in favor of these species. This indicates that climate warming is altering microbial distributions in freshwater environments.

Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by several different herbivores, but the effects of multiple herbivore types on the plant microbiome remain to be determined. Here, we first tested whether feeding by different herbivores (aphids, nematodes and slugs) produces a shift in the rhizosphere bacterial microbiota associated with potato plants. Then, we expanded this question asking whether the identity of the herbivore produces different effects on the rhizosphere microbial community. While we found shifts in microbial diversity and structure due to herbivory, we observed that the herbivore identity does not influence the diversity or community structure of bacteria thriving in the rhizosphere. However, a deeper analysis revealed that the herbivores differentially affected the structure of the network of microbial co-occurrences. Our results have the potential to increase our ability to predict how plant microbiomes assemble and aid our understanding of the role of plant microbiome in plant responses to biotic stress.

Preventive vaccination is currently the most affordable and economical way to reduce morbidity and mortality from many infections, improve quality and human life expectancy with an almost ideal balance of benefits and risks among all medical procedures. The article deals with the reasons for variability of the immune response caused by vaccines, between individuals and between populations, which is of fundamental importance for human health. The authors have presented data indicating a key role of the gut microbiota in the control of the immune response to vaccination. Particular attention is paid to the microbial diversity in different loci of the body. The role of microorganisms in the proper functioning of the body and the formation of a number of pathological conditions is described. Most modern vaccines are live-attenuated, killed / inactivated or subunit (recombinant) vaccines, and they are designed for the parenteral route of administration. Most of these vaccines elicit a weak immune response, especially in the mucous membranes, due to the route of administration and are associated with weak cell-mediated immunity. Therefore, mechanisms that can enhance virus-specific vaccine immunity in infants and children are required, such as the use of more potent or selective immunity-enhancing adjuvants. Some probiotic strains may be considered as promising vaccine adjuvants. This article evaluates the recent clinical studies of probiotics used to enhance vaccine-specific immunity in adults and infants. The present-day knowledge on the role of the probiotic strain Lactobacillus rhamnosus GG with the aim of activating immunity after vaccination are presented.

Fusarium wilt of tomato is widespread throughout China, and the large spread of Fusarium oxysporum f. sp.lycopersici (FOC) in the soil is the main reason. The application of vermicompost provides a...

With the environmental problems brought about by the excessive use of fertilizers and pesticides, numerous biological amendments have been developed and used in recent years. This study, through in-depth analysis of the effects of two different microbial amendments on the microbial diversity in the garlic rhizosphere, provides a theoretical basis and data support for farmers to select microbial amendments. In the experiment, two different microbial amendments were applied to garlic, and its rhizosphere soil was collected after 10, 20, 30, and 40 days. The polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze bacterial diversity in the garlic rhizosphere soil. The total abundance and diversity of microbial flora in the rhizosphere soil of garlic increased after application of microbial amendments to soil or plants. Plant growth was significantly better in the soil treatment than the plant treatment and the water control. The two dominant bacteria of uncultured gamma proteobacterium and Uncultured Gemmatimonadete existed only in the soil treatment. After 40 day of treatment, the abundance in the rhizosphere soil of these four bacterial strains (Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., uncultured gamma proteobacterium, and Pseudomonas boreopolis) was greater in the soil than the plant treatment and the control. The irrigation of microbial amendments not only influenced the structure and abundance of rhizosphere microorganisms, and also promoted the colonization by microorganisms. The five bacterial strains of uncultured gamma proteobacterium, Uncultured Gemmatimonadetes, Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., Pseudomonas boreopolis could facilitate the growth and enhance resistance of garlic, establishing a foundation for the use of microbial amendments and providing new ideas and methods for environmental management and protection.

Blueberry (Vaccinium ssp.) is a perennial shrub belonging to the family Ericaceae, which is highly tolerant of acid soils and heavy metal pollution. In the present study, blueberry was subjected to cadmium (Cd) stress in simulated pot culture. The transcriptomics and rhizosphere fungal diversity of blueberry were analyzed, and the iron (Fe), manganese (Mn), copper (Cu), zinc (Zn) and cadmium (Cd) content of blueberry tissues, soil and DGT was determined. A correlation analysis was also performed. A total of 84 374 annotated genes were identified in the root, stem, leaf and fruit tissue of blueberry, of which 3370 were DEGs, and in stem tissue, of which 2521 were DEGs. The annotation data showed that these DEGs were mainly concentrated in a series of metabolic pathways related to signal transduction, defense and the plant–pathogen response. Blueberry transferred excess Cd from the root to the stem for storage, and the highest levels of Cd were found in stem tissue, consistent with the results of transcriptome analysis, while the lowest Cd concentration occurred in the fruit, Cd also inhibited the absorption of other metal elements by blueberry. A series of genes related to Cd regulation were screened by analyzing the correlation between heavy metal content and transcriptome results. The roots of blueberry rely on mycorrhiza to absorb nutrients from the soil. The presence of Cd has a significant effect on the microbial community composition of the blueberry rhizosphere. The fungal family Coniochaetaceae, which is extremely extremelytolerant, has gradually become the dominant population. The results of this study increase our understanding of the plant regulation mechanism for heavy metals, and suggest potential methods of soil remediation using blueberry.

Analysis of water bodies, such as rivers and lakes can provide an insight into their intrinsic composition and potential impact on the environment. Water samples collected from four designated sites in Idah River, were assessed for their physicochemical parameters and microbial diversity using standard procedures. The temperature from all sites was 26.00°C and the pH ranged from 6.93 to 7.08. Turbidity values ranged between 32.00 and 38.00 NTU, while dissolved oxygen ranged between 6.28 and 9.28 ppm. Heavy metals, such as Selenium and Arsenic (with peak values of 0.10 and 0.09 ppm, respectively) were detected in the river. However, dissolved oxygen, arsenic and turbidity values across all sites exceeded the maximum limit set by World Health Organisation and the Standard Organisation of Nigeria. The total heterotrophic bacterial counts showed excessive bacterial load from all sample sites, while pathogenic bacteria, including Escherichia coli, Klebsiella and Shigella species, were isolated from regions with intense anthropogenic activities along the river, indicative of microbial pollution. Fungal studies identified the presence of Fusarium, Aspergillus and Trichoderma species as the most abundant in the river. Obtained results showed that Idah River is exposed to heavy metal seepage and subject to microbial contamination. Therefore, continuous monitoring and better management of the river body is recommended to prevent disease outbreak. Key words: Aquatic ecosystems, Idah River, microbial diversity, physicochemical analysis.

The construction of amplified 16S rRNA gene libraries has been a major methodology for bacterial/archaeal environmental community profiling for decades. Over the years, a variety of alternative pri...

BACKGROUND AND OBJECTIVES The skin microbiota partly determined by epidermal barrier plays an important role in acne vulgaris and intense pulsed light (IPL) has been verified as a safe and effective therapeutic option for this disease. Nevertheless, the exact role of the IPL treatment on the skin microbiota and epidermal barrier for patients with acne vulgaris remains unclear. This article was designed to solve this problem. STUDY DESIGN/MATERIALS AND METHODS Nineteen healthy controls and 20 patients with mild to moderate acne were enrolled in this study, who received IPL treatment for 12 weeks. The epidermal barrier and skin samples were collected at baseline and after treatment. The microbial diversity was analyzed based on a high-throughput sequencing approach, which targets the V3-V4 region of the bacteria 16S ribosomal RNA genes. RESULTS After treatment of IPL, the Global Acne Grading System (GAGS) scores, sebum, sclererythrin, and red area of patients were significantly improved by IPL treatment (P

Rice beverages are traditionally prepared and consumed popularly by the different ethnic groups of North East India and claimed to have several health benefits. In an attempt to validate the traditional claims, effects of different fractions of the beverage were studied using mouse model. To investigate its effects on behavior, mice were treated with different fractions of rice beverage that included the beverage as a whole, insoluble and soluble fractions. Intragastric treatments of these fractions were given to the mice (n = 6 per group) for 30 days, and behavioral studies were performed on elevated plus and Y maze to evaluate anxiety and spatial memory, respectively. Next-generation sequencing of metagenomic DNA of the beverage indicated the presence of 157 OTUs, and 26 bacterial genera were dominant with an abundance of 0.1%. The insoluble fraction and the whole beverage treatments reduced the anxiety-like symptoms in animals indicating the probable role of microbes. Spatial memory improved in all the treatments compared to the control, of which the rice beverage treatment showed the highest levels (p < 0.05). Gas chromatography and mass spectroscopy-based metabolite profiling of the beverage revealed 10 alcohols, 29 sachharides, 43 acids, and 13 amino acids. Findings of this study suggest a positive effect of rice beverage on anxiety and spatial memory of mice, justifying the claims by ethnic communities on its role on mood regulation.

High-throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence-activated cell sorting (FACS)-based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC-QTOF-MS/MS-guided fractionation and microplate-based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.

Crustaceans such as prawn and shrimp are nutritious seafood and contain high level of protein. However, due to high-water activity and neutral pH, crustaceans are highly susceptible to spoilage microorganisms that are present as normal microbiota. Development stages and culture environment, diet composition and storage temperature were highlighted in this review as factors that contribute to the composition of microbial communities present in prawn and shrimp. However, the use of biofloc technology during culturing/farming could help to reduce the microbial load at pre-harvest level while the use of neutralized oxidized water could be used to further reduce microbial load during post-harvest handling of the seafood. The use of both biofloc technology and neutral electrolyzed oxidizing water would therefore help to preserve the quality and shelf-life of prawn and shrimp.

In Xinjiang, China, traditional handmade cheese is made from fresh milk under natural environmental conditions and is a common fermented dairy product in the region. Due to differences in production methods between regions, the research conducted on the bacterial diversity of traditional handmade cheese is not comprehensive. Hence, little is known about the relationship between bacteria and cheese quality. Therefore, in this study, cheese samples from Tarbagatay Prefecture, Xinjiang, were chosen for investigation. The bacteria in 17 cheese samples were analyzed by sequencing 16S rRNA using Illumina MiSeq technology. The results showed that there were two dominant bacterial phyla and six dominant bacterial genera in the cheeses. Of these, Lactobacillus and Lactococcus displayed the most significant positive correlation with cheese quality. This study provides data to support the improvement of traditional cheese quality via microbial diversity and lays a foundation for the industrialization of traditional cheese production., Traditional cheese of Xinjiang, China, has a long history and the consumption demand is also increasing. In recent years, people pay more and more attention to the quality and microbial diversity of Xinjiang traditional cheese, which also contains a variety of microbial resources. The results showed that the bacteria in Xinjiang traditional cheese were rich and diverse, and the core dominant genera were Lactobacillus, Streptococcus, Lactococcus, Staphylococcus, Enterococcus, and Acetobacters. This study provides a basis for the industrialization of traditional fermented dairy products.

Rhizobacteria have huge potential for biocontrol activity against many plant pathogens. Isolation and identification are therefore crucial to understand their microbial diversity and ecological imp...

Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen

The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting (mesophilic, thermophilic, cooling and maturation phases). In addition, the physicochemical parameters of the composting system were determined in this study. The fermentation time of the thermophilic period was prolonged with the addition of urea or urea combined with a microbial agent. The ratio of C/N and germination index variation indicated that the additives were favorable for composting, because the additives directly changed the physicochemical properties of the compost and had effects on the diversity and abundance of bacteria and fungi. The abundance of operational taxonomic units (OTUs), diversity index (Shannon) and richness index (Chao1) of fungi and bacteria were found to significantly increase when urea+microbial agents were added to straw in the thermophilic phase. The relative abundance of the predominant bacteria and fungi at the phylum and genus levels differed during different composting phases. The abundance of the phyla Firmicutes and Proteobacteria declined in the order of treatments SNW>SN>S (S is straw only compost; SN is straw+5 kg t−1 urea compost; and SNW is straw+5 kg t−1 urea+ 1 kg t−1 microbial agent compost) in the thermophilic phase. The abundance of the genera Staphylococcus, Bacillus and Thermobifida followed the same order in the mesophilic phase. Ascomycota accounted for more than 92% of the total fungal sequences. With the progression of the composting process, the abundance of Ascomycota decreased gradually. The abundance of Ascomycota followed the order of S>SN>SNW during the thermophilic phase. The abundance of Aspergillus accounted for 4–59% of the total abundance of fungi and increased during the first two sampling periods. Aspergillus abundance followed the order of SNW>SN>S. Additionally, principal component analysis (PCA) revealed that the community compositions in the straw and straw+urea treatments were similar, and that the bacterial communities in treatments S, SN and SNW in the mesophilic phase (at day 1) were different from those observed in three other phases (at days 5, 11, and 19, respectively), while the fungal communities showed only slight variations in their structure in response to changes in the composting process. Canonical correlation analysis (CCA) and redundancy analysis (RDA) showed that total carbon (TC), NO3−-N (NN), electrical conductivity (EC) and pH were highly correlated with community composition. Therefore, this study highlights that the additives are beneficial to straw composting and result in good quality compost.

Urechis unicinctus is an important commercial and ecological invertebrate that has potential applications in the study of marine invertebrate evolution and marine pharmaceutical development. Here we analyzed the intestinal microbial diversity of U. unicinctus from 2 different habitats using 16S rDNA 454 high-throughput sequencing. The dominant phyla were Proteobacteria, Bacterioidetes, Firmicutes, and Actinobacteria in gut samples of U. unicinctus, which significantly differed from those in its 2 habitats (i.e. intertidal mudflat and pond polyculture). Exceptions were Proteobacteria, Firmicutes and Bacterioidetes, which were the dominant phyla in the sediment and water samples. The top 15 genera in the gut samples did not show any significant differences between the 2 habitats. Functional analysis of the intestinal microbial community showed that metabolism, including carbohydrate and amino acid metabolism, was the most important function. Methane metabolism was one of the main components of energy metabolism. The gut microbes also played an important role in environmental and genetic information processing, cellular processes, etc. These findings provide an understanding of gut microbiome composition and diversity in U. unicinctus from 2 different habitats. Our results can inform the management of animal health in U. unicinctus farming activities and further gut microecology research.

Devdarha is a tropical dry deciduous forest situated in Padampur subdivision of Bargarh district Odisha India. It is present near to Odisha Chhattisgarh border having Latitude 21.12035˚N and longitude 83.04503˚E. The forest is bisected by the Ong River. In this investigation there was an attempt had been made to analyze the physicochemical property of soil, Bacterial diversity of forest soil and Dominant economically important plant species found in Devdarha. In this investigation, it was found that soil was slightly acidic soil having a pH 6.8. High water holding capacity, moisture content, organic carbon content, NPK content indicate that it was fertile soil and luxuriant for plant growth. There were four different species of bacteria found among them Rhizobium spp. important for nitrogen fixation. Here we had found 32 economically important plant species belonging to 17 families. This type of investigation gives us an idea about the interaction of biotic and abiotic components of a typical forest ecosystem.

Many biotic and abiotic processes contribute to nitrous oxide (N2 O) production in the biosphere, but N2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N2 O reductase enzyme, NosZ, responsible for N2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N2 O reducers could play an important, previously unrecognized role in controlling N2 O emissions for several reasons, including: (1) the consumption of N2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N2 O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2 O reducers in regulating soil N2 O emissions.

This study explored the differences in the microbial diversity and physicochemical properties of mushroom residue and cow manure to provide a theoretical basis for the use of mushroom residue as cow bedding. High-throughput sequencing was used to analyze the bacterial community composition of mushroom residue and cow manure bedding and determine the physical and chemical properties of these different bedding materials. The results showed that the bacterial communities in the two types of bedding materials could be categorized into 6 classes, 13 orders, 32 families, and 48 genera. The dominant genus in the mushroom residue bedding samples after use by cows was Lactobacillus (36.37%) followed by Corynebacterium (22.15%). The dominant group in the cow manure bedding samples after use was "other" (28.8%), followed by Solibacillus (8.76%). The different bedding materials contained varying number of bacterial species. After use, 499 bacterial species were present in the cow manure bedding, while only 345 bacterial species were present in the mushroom residue bedding. The utilization rate of the mushroom residue bedding by dairy cows was 79%, whereas that of the cow manure bedding was 61%. The results of this study provide a theoretical basis for the application of mushroom residue bedding for dairy cows.

Organic and inorganic materials migrate downstream and have important roles in regulating environmental health in the river networks. However, it remains unclear whether and how a mixture of materials (i.e., microbial species) from various upstream habitats contribute to microbial community coalescence upstream of a dam. Here we track the spatial variation in microbial abundance and diversity in the Three Gorges Reservoir based on quantitative PCR and 16S rRNA gene high-throughput sequencing data. We further quantitatively assess the relative contributions of microbial species from mainstem, its tributaries, and the surrounding riverbank soils to the area immediately upstream of the Three Gorges Dam (TGD). We found an increase of microbial diversity and the convergent microbial distribution pattern in areas immediately upstream of TGD, suggesting this area become a new confluence for microbial diversity immigrating from upstream. Indeed, the number of shared species increased from upstream to TGD but unique species decreased, indicating immigration of various sources of microbial species overwhelms local environmental conditions in structuring microbial community close to TGD. By quantifying the sources of microbial species close to TGD, we found little contribution from soils as compared to tributaries, especially for sites closer to TGD, suggesting tributary microbes have greater influence on microbial diversity and environmental health in the Three Gorges Reservoir. Collectively, our results suggest that tracking microbial geographic origin and evaluating accumulating effects of microbial diversity shed light on the ecological processes in microbial communities and provide information for regulating aquatic ecological health.

Sludge samples were collected from a wastewater treatment plant in Nigeria for characterization and evaluation for agricultural applications. Conventional and Molecular techniques were adopted for the isolation and identification of indigenous microorganisms and resulting isolates were characterized and identified by consulting Bergey’s manual of determinative bacteriology and subjected to further screenings to assess their biofertilizer potential using standard microbiological techniques. The viable cells obtained were enumerated and were found to be in the range of 1.03 ± 0.09 x103 cfu/g to 7.45 ± 0.78 x103 cfu/g for heterotrophic Bacteria and 1.63 ± 0.74 x103 cfu/g for fungal community. The Molecular analysis carried out revealed a rich assemblage of diverse species of microorganisms with Bacteria (99.40%) being the most dominant group, followed by Fungi (0.39%) and others (0.21%). Thirty (30) isolates belonging to four (4) Phyla was recovered culturally and identified with Firmicutes 9(30%) being the most dominant group, followed by Proteobacteria 8(26.7%) and Zygomycota 1(3.33%) was the least dominant. The phosphate solubilization index range from 0.86 to 6.3 for bacterial and 2.5 to 3.8 for fungal isolates respectively. The molecular analysis also revealed microbes adept at improving soil fertility to include those in the order Rhizobiales and Actinomycetales. Although pathogens are of a concern in the land application of sludge, our findings have revealed rich microbial consortia of heterotrophic microorganisms whose beneficial attributes can be harnessed to produce nutrient rich biofertilizer and soil amendment.

In desert ecosystems, the desertification process is characterized by increasing attenuation of plant productivity and deterioration of soil habitats, leading to enhanced environmental stress gradients for soil microbiomes. Despite the significance of microbial communities for multifunctionality in terrestrial ecosystems, the feedback dynamics of microbiomes and their contributions to maintaining deep soil (20–100 cm) multifunctionality as desertification progresses have yet to be evaluated. Here, we used three sites with different desertification stages and investigated the variation trends of microbiomes in soil profiles (0–100 cm) and their contributions to regulating multifunctionality. The multifunctionality did not exhibit a significant difference between superficial (0–20 cm) and deep soils and slightly decreased as depth increased throughout the entire profile. Results from alpha‐ and beta‐diversity analysis of soil microbiomes suggested that bacterial communities received on average more positive and progressive feedback from desertification development than fungal and archaeal communities. Particular microbial clades rather than total microbial diversity best predict and explain the vertical profile variation in soil multifunctionality in desert ecosystems. Microbial clades within Acidobacteria could be targeted for future soil‐focussed, bottom‐up desertification control studies.

Gut microbiota plays important roles in host nutrition, metabolism and immunity, and is affected by multiple factors. However, the understandings of the gut microbiota in pigs within different breeds, growth periods and genders from a large cohort remain largely undefined. In the present study, the characteristics of the gut microbiota in 120 pigs of different breeds, growth periods and genders were investigated using the Illumina MiSeq PE300 combined with QIIME2 platform. A total of 7 388 636 raw reads and 16 411 features were obtained. Additionally, the microbial diversity, compositions and phenotypes were described. 66.53% microbiota belonged to the top 10 most abundant genera (pan gut bacteria), and 28 species were commonly identified (core gut bacteria, commonality ≥ 75%) among the pigs. Besides, the correlations within pan and core gut microbiota were firstly investigated. The metagenomic function was predicted by using PICRUSt2. Furthermore, the explanatory effects of the influencing factors suggested that growth period was the greatest contributor to the gut microbiota in pigs. These results expanded our knowledge of mammalian gut microbiota within different influencing factors and microbial-related biological features in swine, which contributes to improving animal production and assisting animal model research.

Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these “dynamic pulses of microbial life” for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

Soybean paste is the oldest condiment with a unique flavor worldwide, and is widely used as a seasoning ingredient in authentic Asian cuisine. The metabolic activity of the microorganisms that exist in different ecological niches in fermentation donates its characteristic of flavor. It’s significant to elucidate structure and functional microbiota repertoires, as well as environmental associations between the diversity and structure of both bacterial and fungal communities for guaranteeing the quality in soybean paste manufacturing. In this review, procession of fermentation, microbial diversity, functional microbiota and correlation between microbiota and flavor are summarized. Exploring the mechanism of microbial communities involved in soybean paste fermentation is benefit for improving quality and safety in manufacture.

Contamination of food products with the foodborne pathogen Listeria monocytogenes may occur in the food processing environment. Many bacterial species co-exist in this environment and can interact in multispecies biofilms. Recent studies have shed light on the composition of microbial communities present in the same ecological habitat as L. monocytogenes. Others have aimed at identifying competitive or cooperative interactions between L. monocytogenes and other species in mixed-species biofilms. Both microbial composition and interactions may be differently influenced even by different strains belonging to the same species. Novel methodology based on recent advances in sequencing technologies promise to provide new insights into how the resident microbiota may influence the presence of L. monocytogenes in food industry environments.