Divergence of phyllosphere microbial communities between females and males of the dioecious Populus cathayana

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacteria and fungi microbiota, such as bacteria Gemmata (5.41%) and fungi Pringsheimia (0.03%) in females, and bacteria Chitinophaga (0.009%) and fungi Phaeococcomyces (0.02%) in males. Significant differences in the relative abundance of bacterial phyla Proteobacteria, Planctomycetes and the fungal phyla Ascomycota, Basidiomycota (P < 0.05) were also found between females and males. Some bacterial genera Spirosoma and Amnibacterium, and fungal genera Venturia, Suillus, and Elmerina were significantly enriched in males (P < 0.05). In contrast, fungal genera Phoma and Aureobasidium were found significantly higher in females than in males (P < 0.05). The mineral, inorganic and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08% and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.

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Corynebacterium Comparative Genomics Reveals a Role for Cobamide Sharing in the Skin Microbiome

10.1101/2020.12.02.407395 ◽

2020 ◽

Author(s):

Mary Hannah Swaney ◽

Lindsay R Kalan

Keyword(s):

Comparative Genomics ◽

Microbial Communities ◽

Community Dynamics ◽

De Novo ◽

Skin Barrier ◽

Skin Microbiome ◽

Bacterial Phyla ◽

Host Interactions ◽

Complex Interactions ◽

Associated Species

ABSTRACTThe human skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. Recent studies have begun unraveling the complex interactions within skin microbial communities, shedding light on the invaluable role that skin microorganisms have in maintaining a healthy skin barrier. While the Corynebacterium genus is a dominant taxon of the skin microbiome, relatively little is known how skin-associated Corynebacteria contribute to microbe-microbe and microbe-host interactions on the skin. Here, we performed a comparative genomics analysis of 71 Corynebacterium species from diverse ecosystems, which revealed functional differences between host- and environment-associated species. In particular, host-associated species were enriched for de novo biosynthesis of cobamides, which are a class of cofactor essential for metabolism in organisms across the tree of life but are produced by a limited number of prokaryotes. Because cobamides have been hypothesized to mediate community dynamics within microbial communities, we analyzed skin metagenomes for Corynebacterium cobamide producers, which revealed a positive correlation between cobamide producer abundance and microbiome diversity, a trait associated with skin health. We also provide the first metagenome-based assessment of cobamide biosynthesis and utilization in the skin microbiome, showing that both dominant and low abundant skin taxa encode for the de novo biosynthesis pathway and that cobamide-dependent enzymes are encoded by phylogenetically diverse taxa across the major bacterial phyla on the skin. Taken together, our results support a role for cobamide sharing within skin microbial communities, which we hypothesize mediates community dynamics.

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Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

PeerJ ◽

10.7717/peerj.9376 ◽

2020 ◽

Vol 8 ◽

pp. e9376

Author(s):

Huanhuan Gao ◽

Xiangtian Yin ◽

Xilong Jiang ◽

Hongmei Shi ◽

Yang Yang ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Eastern China ◽

Grape Berry ◽

Wine Quality ◽

Bacterial Phyla ◽

Sour Rot ◽

Bacteria And Fungi ◽

Polymicrobial Disease

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

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Animal soil food web complexity triggers shifts in microbial communities, including PAH degraders, but without clear effects on phenanthrene phytoremediation

10.1101/2021.12.14.472730 ◽

2021 ◽

Author(s):

Sara Correa-García ◽

Vincenzo Corelli ◽

Julien Tremblay ◽

Jessica Ann Dozois ◽

Eugenie Mukula ◽

...

Keyword(s):

Food Web ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Fungal Communities ◽

Soil Food Web ◽

Experimental Conditions ◽

Bacterial Phyla ◽

Soil Microbial ◽

Degradation Rates ◽

Food Web Complexity

The aim of this study was to determine whether the complexity of the animal soil food web (SFWC) is a significant factor influencing the soil microbial communities, the productivity of the willow, and the degradation rates of 100 mg kg-1 phenanthrene contamination. The SFWC treatment had eight levels: just the microbial community (BF), or the BF with nematodes (N), springtails (C), earthworms (E), CE, CN, EN, CEN. After eight weeks of growth, the height and biomass of willows were significantly affected by the SFWC, whereas the amount of phenanthrene degraded was not affected, reaching over 95% in all pots. SFWC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFWC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many PAH degraders. These SFWC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to the Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFWC treatments. Overall, our results suggest that, under our experimental conditions, SFWC does not affect significantly willow phytoremediation outcomes.

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Soil Fungal Communities Investigated by Metabarcoding within Simulated Forensic Burial Contexts

10.21203/rs.2.22871/v1 ◽

2020 ◽

Author(s):

Noemi Procopio ◽

Stefano Ghignone ◽

Samuele Voyron ◽

Marco Chiapello ◽

Anna Williams ◽

...

Keyword(s):

Microbial Communities ◽

Experimental Studies ◽

Soil Microbial Communities ◽

Fungal Communities ◽

Post Mortem ◽

Morphological Examination ◽

Soil Microbial ◽

Fungal Biomarkers ◽

Bacteria And Fungi ◽

Pmi Estimation

Abstract Background One of the most debated questions in forensic science is the estimation of the post-mortem interval (PMI). Despite the large amount of research currently performed to improve the PMI estimation, there is still the need for additional improvements, particularly in cases of severely decomposed buried remains. A novel alternative to the morphological examination of the remains is the analysis of the soil microbial communities. Bacteria and fungi are ubiquitous and can be found in the soil and in/on the corpses, and their shifts in populational compositions present at different PMIs may reveal insights for PMI estimation. Despite it already having been revealed that bacteria might be good candidates for this type of analysis, there are knowledge gaps for this type of application when dealing with fungal communities. For this reason, we performed the metabarcoding analysis of the mycobiome present in the soil after prolonged decomposition times, from one- to six-months, targeting both the Internal Transcribed Spacer (ITS) 1 and 2, to elucidate which of the two was more suitable for this purpose. Results Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs and the presence of specific trends associated with specific PMIs, such as the increase of the Mortierellomycota taxa after four- and six-months post-mortem and of Ascomycota particularly after two months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited amount of taxa specifically associated with the presence of the mammalian carcasses and not present in the control soil, showing that the overall the taxa which are contributing the most to the changes in the community originate from the soil and are not introduced by the carrion, extending the potential to perform comparisons with other experimental studies with different carrion species. Conclusions This study has been the first one conducted on gravesoil, and sets the baseline for additional studies, showing the potential to use fungal biomarkers in combination with bacterial ones to improve the accuracy of the PMI predictive model based on the shifts in the soil microbial communities.

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Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China

Soil Research ◽

10.1071/sr19204 ◽

2020 ◽

Vol 58 (1) ◽

pp. 35

Author(s):

Lin Gao ◽

Rui Wang ◽

Jiaming Gao ◽

Fangming Li ◽

Guanghua Huang ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Soil Samples ◽

Fungal Communities ◽

Sequencing Technology ◽

Operational Taxonomic Units ◽

Tobacco Cultivation ◽

Bacteria And Fungi ◽

Disease Suppressive Soil ◽

Conducive Soil

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.

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The distribution of active β-glucosidase-producing microbial communities in composting

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0368 ◽

2017 ◽

Vol 63 (12) ◽

pp. 998-1008 ◽

Cited By ~ 11

Author(s):

Xiangyun Zang ◽

Meiting Liu ◽

Han Wang ◽

Yihong Fan ◽

Haichang Zhang ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Cellulose Degradation ◽

Cellulose Hydrolysis ◽

Bacterial Phyla ◽

Metabolic Activities ◽

Bacteria And Fungi ◽

A Minor ◽

Dominant Bacteria ◽

Global Carbon

The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure – rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus–Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.

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Microbial Community Analysis of Rhizosphere of Healthy and Wilted Pepper (Capsicum Annuum L.) in An Organic Farming System

10.21203/rs.3.rs-575849/v1 ◽

2021 ◽

Author(s):

Román González-Escobedo ◽

Laila N. Muñoz-Castellanos ◽

Zilia Y. Muñoz-Ramirez ◽

César Guigón López ◽

Graciela Dolores Avila-Quezada

Keyword(s):

Microbial Communities ◽

Capsicum Annuum ◽

Microbial Community Analysis ◽

Fungal Communities ◽

Economic Losses ◽

Individual Species ◽

Internal Transcribed Spacer Region ◽

Bacterial Phyla ◽

Α Diversity ◽

Significant Difference

Abstract Rhizosphere microorganisms play an important role in the growth and health of plants. Around the world, diverse soil-borne pathogens attack Capsicum annuum causing significant damage and economic losses; however, very little is known about how rhizosphere microbial communities are altered by infestation with root pathogens. This work aimed to determine whether the diversity and structure of microbial communities in the rhizosphere soil of C. annuum plants is significantly changed by wilt disease. We used 16S rRNA for bacteria and the internal transcribed spacer region for fungi, to characterize the rhizosphere microbiomes of healthy and wilted plants. The most abundant bacterial phyla were Proteobacteria and Gemmatimonadetes, while the most abundant fungal phyla were Ascomycota and Mucoromycota. The bacterial α-diversity did not show significant differences in richness and diversity, but did show a significant difference in evenness and dominance of species. Rare taxa were present in both healthy and wilted conditions with relative abundances < 1%. In the fungi, all evaluated estimators showed a significant reduction in the wilted condition. The β-diversity showed significant differences in the structure of bacterial and fungal communities, which were segregated according to plant health condition. The differential abundance analysis did not show significant results in the bacterial communities; however, in the fungal communities, Rhizopus, Thanatephorus, Curvularia, Fusarium, Cladosporium, and Alternaria were more abundant in the rhizosphere of wilted than healthy plants. Species from these genera have been previously reported as phytopathogens of several plants, including in reports on individual species as disease agents in C. annuum.

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Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration

10.21203/rs.2.18239/v2 ◽

2020 ◽

Author(s):

Jing Li ◽

Xiaoyue Zhang ◽

Lin Xiao ◽

Ke Liu ◽

Yue Li ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Soil Microbial Communities ◽

Fungal Communities ◽

Yeast Genus ◽

Soil Microbial ◽

Physicochemical Factors ◽

Permanent Loss ◽

Relative Abundances ◽

Bacteria And Fungi

Abstract Background: Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on the physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the communities and their correlation with environmental factors, and compare community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa.Results: The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. Conclusion: The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

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Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

Microorganisms ◽

10.3390/microorganisms9010064 ◽

2020 ◽

Vol 9 (1) ◽

pp. 64

Author(s):

Maija Nuppunen-Puputti ◽

Riikka Kietäväinen ◽

Lotta Purkamo ◽

Pauliina Rajala ◽

Merja Itävaara ◽

...

Keyword(s):

Significant Proportion ◽

Debaryomyces Hansenii ◽

Fungal Communities ◽

Fungal Colonization ◽

Rock Surface ◽

Mica Schist ◽

Deep Subsurface ◽

Bacterial Phyla ◽

In Situ Conditions

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

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Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽

10.3390/atmos12070809 ◽

2021 ◽

Vol 12 (7) ◽

pp. 809

Author(s):

Sen Wang ◽

Wanyu Liu ◽

Jun Li ◽

Haotian Sun ◽

Yali Qian ◽

...

Keyword(s):

Seasonal Variation ◽

Relative Abundance ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Fine Particulate Matter ◽

Ecological Functions ◽

Factors Affecting ◽

Bacterial Phyla ◽

Variation Characteristics ◽

Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

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