Changes in structure and function of bacterial and fungal communities in open composting of Chinese herb residues

In this study, dynamic changes in bacterial and fungal communities, metabolic characteristics, and trophic modes in Chinese herb residues open composting for 30 days were analyzed by using high-throughput sequencing, PICRUSt, and FUNGuild, respectively. Bacillaceae and Basidiomycota predominated at the early composting stage, while Proteobacteria and Ascomycota became the dominant phyla during the active phase. Aerobic composting had a significant effect on bacterial metabolic characteristics and fungal trophic modes over the composting time. The function of the bacterial communities changed from environmental information processing to metabolism. Fungal communities changed as well, with the pathogenic fungi decreasing and wood saprotrophs increasing. These results indicated that open composting of Chinese herb residues not only influenced microbial community structure but also changed metabolic characteristics and trophic modes, which became the internal dynamics of composting.

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Bacterial Diversity and Community in Regional Water Microbiota between Different Towns in World’s Longevity Township Jiaoling, China

Diversity ◽

10.3390/d13080361 ◽

2021 ◽

Vol 13 (8) ◽

pp. 361

Author(s):

Lei Wu ◽

Xinqiang Xie ◽

Jumei Zhang ◽

Yu Ding ◽

Qingping Wu

Keyword(s):

16S Rrna ◽

High Throughput Sequencing ◽

The Other ◽

Rrna Gene ◽

Metabolic Characteristics ◽

Kegg Pathways ◽

Healthy Longevity ◽

And Function ◽

Regional Water

Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.

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Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

10.21203/rs.2.17468/v1 ◽

2019 ◽

Author(s):

Ya Dai ◽

Xin-Yu Li ◽

Yan Wang ◽

Cai-Xia Li ◽

Yuan He ◽

...

Keyword(s):

Medicago Sativa ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Pathogenic Fungi ◽

Fungal Communities ◽

High Abundance ◽

Tibet Plateau ◽

Grass Species ◽

Elymus Sibiricus ◽

Qinghai Tibet Plateau

Abstract Background: The grasses in adverse environment such as Qinghai-Tibet Plateau are hypothesized to survive the harsh climate in part upon their seed-borne microorganisms, and yet the characteristics of the grass seed microbial communities remain undetermined. Here, we assessed the seed microbial communities of three native gramineous grass species (Avena sativa, Elymus sibiricus and Elymus dahuricus) and four candidate legumes (Vicia villosa, Trifolium repens, Trifolium pretense and Medicago sativa) on the Qinghai-Tibet Plateau by high-throughput sequencing. Results: A total of 1,013 bacterial operational taxonomic units (OTUs) and 922 fungal OTUs were observed. The OTUs that shared in all the samples were in high abundance but with different relative abundances. The majority of bacterial sequences were assigned to Proteobacteria (54~90%) and Firmicutes (5~41%), and the fungal communities were mainly composed of Ascomycota (23~96%) and Basidiomycota (2~11%). The fungal communities were more affected by host genetic distance than bacteria. The three gramineous grasses were speculated to survive the adversity partly due to their high abundance of beneficial bacteria like Pantoea or Bacillus, and non-pathogenic fungi like Candida or unclassified Helotiaceae. Also enriched with these potential beneficial taxa, the four leguminous grasses may be competent to adapt the Qinghai-Tibet Plateau stress. Furthermore, the higher tolerance grasses (Elymus sibiricus and Elymus dahuricus) possessed a greater number of growth-promoting and tolerance bacterial and non-pathogenic fungi. Conversely, the less tolerance grass Medicago sativa contained lower levels of such microorganisms, and showed higher abundance of pathogenic taxa. Furthermore, the isolated Bacillus subtilis or Pantoea agglomerans could more probably promote seeding growth of hosts with lower abundance of them, while inhibit if the endo-abundance of was high. Conclusions: Seed-resident microbiome structure of the four cold-tolerance legumes and three Qinghai-Tibet Plateau gramineae is host dependent and related to stress resistance. It also has a strong influence on the response of seedlings to biological seed treatments. This study provides valuable data for studying plant resilience, identifying more biocontrol strains, maximizing microbial functions in ‘smart farming’ practices.

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Host-environment interplay shapes fungal diversity in mosquitoes

10.1101/2020.12.01.407494 ◽

2020 ◽

Author(s):

Patil Tawidian ◽

Kerri L. Coon ◽

Ari Jumpponen ◽

Lee W. Cohnstaedt ◽

Kristin Michel

Keyword(s):

Aedes Albopictus ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Health Concern ◽

Dominant Factor ◽

Aquatic Environments ◽

Research Attention ◽

Fungal Entomopathogens ◽

And Function ◽

The Impact

ABSTRACTMosquito larvae encounter diverse assemblages of bacteria (i.e. ‘microbiota’) and fungi (i.e. ‘mycobiota’) in the aquatic environments they develop in. However, while a number of studies have addressed the diversity and function of microbiota in mosquito life history, relatively little is known about mosquito-mycobiota interactions outside of several key fungal entomopathogens. In this study, we used high-throughput sequencing of ITS2 gene amplicons to provide the first simultaneous characterization of the mycobiota in field-collected Aedes albopictus larvae and their associated aquatic environments. Our results reveal unprecedented variation in mycobiota among adjacent but discrete larval breeding habitats. Our results also reveal distinct mycobiota assembly in the mosquito gut versus other tissues, with gut-associated fungal communities being most similar to those present in the environment where larvae feed. Altogether, our results identify the environment as the dominant factor shaping mosquito mycobiota with no evidence of environmental filtering of the gut mycobiota. These results also identify mosquito feeding behavior and fungal mode of nutrition as potential drivers of tissue-specific mycobiota assembly after environmental acquisition.IMPORTANCEThe Asian tiger mosquito, Aedes albopictus, is the dominant mosquito species in the USA and an important vector of arboviruses of major public health concern. One aspect of mosquito control to curb mosquito-borne diseases has been the use of biological control agents such as fungal entomopathogens. Recent studies also demonstrate the impact of mosquito-associated microbial communities on various mosquito traits, including vector competence. However, while much research attention has been dedicated to understanding the diversity and function of mosquito-associated bacterial communities, relatively little is known about mosquito-associated fungal communities. A better understanding of the factors that drive mycobiota diversity and assembly in mosquitoes will be essential for future efforts to target mosquito micro- and mycobiomes for mosquito and mosquito-borne disease control.

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New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities

PeerJ ◽

10.7717/peerj.11340 ◽

2021 ◽

Vol 9 ◽

pp. e11340

Author(s):

Xiaoting Wei ◽

Fengyan Jiang ◽

Bing Han ◽

Hui Zhang ◽

Ding Huang ◽

...

Keyword(s):

Climate Warming ◽

High Throughput Sequencing ◽

Terrestrial Ecosystem ◽

Fungal Communities ◽

Host Responses ◽

Tibet Plateau ◽

Ecosystem Structure ◽

Suitable Habitats ◽

And Function ◽

Endophytic Community

Plant adaptation under climate changes is critical to the maintenance of terrestrial ecosystem structure and function. Studying the response of the endophytic community to climate warming is a novel way to reveal the mechanism of host environmental adaptability because of the prominent role endophytes play in host nutrient acquisition and stress tolerance. However, host performance was generally neglected in previous relevant research, which limits our understanding of the relationships between the endophytic community and host responses to climate warming. The present study selected two plants with different responses to climate warming. Elymus nutans is more suitable for growing in warm environments at low altitude compared to Kobresia pygmaea. K. pygmaea and E. nutans were sampled along an altitude gradient in the natural grassland of Qinghai-Tibet Plateau, China. Root endophytic bacterial and fungal communities were analyzed using high throughput sequencing. The results revealed that hosts growing in more suitable habitats held higher endophytic fungal diversity. Elevation and host identity significantly affected the composition of the root endophytic bacterial and fungal community. 16S rRNA functional prediction demonstrated that hosts that adapted to lower temperatures recruited endophytic communities with higher abundance of genes related to cold resistance. Hosts that were more suitable for warmer and drier environments recruited endophytes with higher abundance of genes associated with nutrient absorption and oxidation resistance. We associated changes in the endophytic community with hosts adaptability to climate warming and suggested a synchronism of endophytic communities and hosts in environmental adaptation.

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Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Diversity ◽

10.3390/d12050172 ◽

2020 ◽

Vol 12 (5) ◽

pp. 172 ◽

Cited By ~ 3

Author(s):

Jelena Lazarević ◽

Audrius Menkis

Keyword(s):

High Altitude ◽

Bark Beetles ◽

Fungal Pathogens ◽

High Throughput Sequencing ◽

Fungal Communities ◽

High Quality ◽

The Balkans ◽

Fungal Community Structure ◽

Growing Conditions ◽

Coniferous Tree Species

Pinus heldreichii is a high-altitude coniferous tree species naturaly occurring in small and disjuncted populations in the Balkans and southern Italy. The aim of this study was to assess diversity and composition of fungal communities in living needles of P. heldreichii specifically focusing on fungal pathogens. Sampling was carried out at six different sites in Montenegro, where 2-4 year-old living needles of P. heldreichii were collected. Following DNA isolation, it was amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. Sequencing resulted in 31,831 high quality reads, which after assembly were found to represent 375 fungal taxa. The detected fungi were 295 (78.7%) Ascomycota, 79 (21.0%) Basidiomycota and 1 (0.2%) Mortierellomycotina. The most common fungi were Lophodermium pinastri (12.5% of all high-quality sequences), L. conigenum (10.9%), Sydowia polyspora (8.8%), Cyclaneusma niveum (5.5%), Unidentified sp. 2814_1 (5.4%) and Phaeosphaeria punctiformis (4.4%). The community composition varied among different sites, but in this respect two sites at higher altitudes (harsh growing conditions) were separated from three sites at lower altitudes (milder growing conditions), suggesting that environmental conditions were among major determinants of fungal communities associated with needles of P. heldreichii. Trees on one study site were attacked by bark beetles, leading to discolouration and frequent dieback of needles, thereby strongly affecting the fungal community structure. Among all functional groups of fungi, pathogens appeared to be an important component of fungal communities in the phyllosphere of P. heldreichii, especially in those trees under strong abiotic and biotic stress.

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The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

Journal of Fungi ◽

10.3390/jof7030194 ◽

2021 ◽

Vol 7 (3) ◽

pp. 194

Author(s):

Carmen Gómez-Lama Cabanás ◽

Antonio J. Fernández-González ◽

Martina Cardoni ◽

Antonio Valverde-Corredor ◽

Javier López-Cepero ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Canary Islands ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Phenological Stage ◽

Mother Plants ◽

Fusarium Wilt Of Banana ◽

Identification And Characterization

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

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Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications

Nature Communications ◽

10.1038/s41467-021-22284-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Feng Chen ◽

Min Bai ◽

Xiaowen Cao ◽

Jing Xue ◽

Yue Zhao ◽

...

Keyword(s):

Fluorescence Imaging ◽

Spatial Organization ◽

High Throughput Sequencing ◽

Dna Amplification ◽

Chromatin Modifications ◽

Dynamic Changes ◽

Recognition Mechanism ◽

Cell Cycles ◽

Dna Modifications ◽

Relationship Of

AbstractExploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.

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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽

10.3390/d11120234 ◽

2019 ◽

Vol 11 (12) ◽

pp. 234 ◽

Cited By ~ 2

Author(s):

Eric A. Griffin ◽

Joshua G. Harrison ◽

Melissa K. McCormick ◽

Karin T. Burghardt ◽

John D. Parker

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tree Diversity ◽

Trophic Levels ◽

Community Diversity ◽

And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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Characterizing fungal communities in medicinal and edible Cassiae Semen using high-throughput sequencing

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2019.108496 ◽

2020 ◽

Vol 319 ◽

pp. 108496 ◽

Cited By ~ 1

Author(s):

Mengyue Guo ◽

Wenjun Jiang ◽

Meihua Yang ◽

Xiaowen Dou ◽

Xiaohui Pang

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Fungal Communities

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The compositional turnover of grapevine-associated plant pathogenic fungal communities are greater among intraindividual microhabitats and terroirs than among healthy and Esca-diseased plants

Phytopathology ◽

10.1094/phyto-05-21-0190-r ◽

2021 ◽

Author(s):

Adrienn Geiger ◽

Zoltán Karácsony ◽

Richárd Golen ◽

Kálmán Zoltán Váczy ◽

József Geml

Keyword(s):

Pathogenic Fungi ◽

Wine Industry ◽

Fungal Communities ◽

Opportunistic Pathogens ◽

Grapevine Trunk Diseases ◽

Esca Disease ◽

Dna Metabarcoding ◽

Trunk Diseases ◽

Fungal Dna ◽

Key Questions

Grapevine trunk diseases (GTD) are a major threat to the wine industry, causing yield loss and dieback of grapevines. While the increasing damage caused by GTDs in recent decades have spurred several studies on grapevine-associated pathogenic fungi, key questions about the emergence and severity of GTDs remain unanswered, including possible differences in plant pathogenic fungal communities in asymptomatic and symptomatic grapevines. We generated fungal DNA metabarcoding data from soil, bark, and perennial wood samples from asymptomatic and symptomatic grapevines sampled in three terroirs. We observed larger compositional differences in plant pathogenic fungi among different plants parts within grapevine plants than among individual grapevines. This is driven by the dominance of GTD-associated fungi in perennial wood and non-GTD pathogens in soil, as well as by the lack of significant differences among asymptomatic and Esca symptomatic grapevines. These results suggest that fungi generally associated with Esca disease belong to the core grapevine microbiome and likely are commensal endophytes and/or latent saprotrophs, some of which can act as opportunistic pathogens on stressed plants. In addition, we found significant compositional differences among sampling sites, particularly in soil, which suggest a certain influence of local edaphic and mesclimatic factors on plant pathogenic fungal communities. Furthermore, the observed differences among terroirs in plant pathogenic fungal communities in grapevine woody parts indicate that environmental factors likely are important for the development of Esca disease and further studies are needed to investigate the abiotic conditions on fungal compositional dynamics in Esca-affected plants.

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