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

PeerJ ◽  
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.

scholarly journals A biomass equation dataset for common shrub species in China

2021 ◽  
Author(s):  
Yang Wang ◽  
Wenting Xu ◽  
Zhiyao Tang ◽  
Zongqiang Xie
Keyword(s):  
Terrestrial Ecosystem ◽  
Structure And Function ◽  
Biomass Estimation ◽  
Ecosystem Structure ◽  
Biomass Equation ◽  
Shrub Species ◽  
Biomass Equations ◽  
Shrub Biomass ◽  
And Function ◽  
Ecosystem Structure And Function

Abstract. Shrub biomass equations provide an accurate, efficient and convenient method in estimating biomass of shrubland ecosystems and biomass of the shrub layer in forest ecosystems at various spatial and temporal scales. In recent decades, many shrub biomass equations have been reported mainly in journals, books and postgraduate's dissertations. However, these biomass equations are applicable for limited shrub species with respect to a large number of shrub species widely distributed in China, which severely restricted the study of terrestrial ecosystem structure and function, such as biomass, production, and carbon budge. Therefore, we firstly carried out a critical review of published literature (from 1982 to 2019) on shrub biomass equations in China, and then developed biomass equations for the dominant shrub species using a unified method based on field measurements of 738 sites in shrubland ecosystems across China. Finally, we constructed the first comprehensive biomass equation dataset for China’s common shrub species. This dataset consists of 822 biomass equations specific to 167 shrub species and has significant representativeness to the geographical, climatic and shrubland vegetation features across China. The dataset is freely available at https://doi.org/10.11922/sciencedb.00641 for noncommercial scientific applications, and this dataset fills a significant gap in woody biomass equations and provides key parameters for biomass estimation in studies on terrestrial ecosystem structure and function.

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

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.

scholarly journals Host-environment interplay shapes fungal diversity in mosquitoes

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.

scholarly journals Gut Bacterial and Fungal Communities of the Wild and Laboratory-Reared Thitarodes Larvae, Host of the Chinese Medicinal Fungus Ophiocordyceps sinensis on Tibetan Plateau

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 327
Author(s):  
Guiqing Liu ◽  
Xuehong Zheng ◽  
Hailin Long ◽  
Zhongchen Rao ◽  
Li Cao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Fungal Species ◽  
Fungal Communities ◽  
Tibet Plateau ◽  
Geographic Locations ◽  
Ophiocordyceps Sinensis ◽  
Abundant Otus ◽  
Significant Difference ◽  
Culture Dependent

By employing a culture-dependent and -independent 16S rRNA and ITS gene high-throughput sequencing analyses, comprehensive information was obtained on the gut bacterial and fungal communities in the ghost moth larvae of three different geographic locations from high-altitude on Tibet plateau and from low-altitude laboratory. Twenty-six culturable bacterial species belonging to 21 genera and 14 fungal species belonging to 12 genera were identified from six populations by culture-dependent method. Carnobacterium maltaromaticum was the most abundant bacterial species from both the wild and laboratory-reared larvae. The most abundant OTUs in the wild ghost moth populations were Carnobacteriaceae, Enterobacteriaceae for bacteria, and Ascomycota and Basidiomycota for fungi. Larval microbial communities of the wild ghost moth from different geographic locations were not significantly different from each other but significant difference in larval microbial community was detected between the wild and laboratory-reared ghost moth. The larval gut of the wild ghost moth was dominated by the culturable Carnobacterium. However, that of the laboratory-reared ghost moth exhibited significantly abundant Wolbachia, Rhizobium, Serratia, Pseudomonas, and Flavobacterium. Furthermore, the larval gut of the wild ghost moth had a significantly higher abundance of Ophiocordyceps but lower abundance of Candida and Aspergillus than that of the laboratory-reared ghost moth.

scholarly journals Decaying Logs Enrich Soil Fungal Communities in the Forest Ecosystem

2021 ◽  
Author(s):  
Qin Wang ◽  
Josep Peñuelas ◽  
Bo Tan ◽  
Zhuang Wang ◽  
Han Li ◽  
...  
Keyword(s):  
Forest Ecosystem ◽  
Soil Fungi ◽  
High Throughput Sequencing ◽  
Coniferous Forest ◽  
Biochemical Properties ◽  
Fungal Communities ◽  
Tibet Plateau ◽  
Sequencing Analysis ◽  
Fungal Community Composition ◽  
Microbial Biomass Nitrogen

Abstract Aims: Soil fungi are crucial drivers of log decomposition in forest ecosystems. The objective of this study was thus to assess the conservation roles of decaying logs on soil fungi.Methods: Five classes of decaying Minjiang fir (Abies faxoniana) logs were incubated on the forest floor in a subalpine coniferous forest on the eastern Qinghai-Tibet Plateau, China, and the fungal communities compositions of the soil under decaying logs were assessed using high-throughput sequencing. Results: A total of 4321 operational taxonomic units (OTUs) were detected by Illumina MiSeq sequencing analysis. Basidiomycota and Ascomycota were dominant phyla regardless of log decay classes. With the log decomposition, the proportion of arbuscular mycorrhiza, wood saprotroph and saprotroph increased, but that of ectomycorrhiza decreased. Moreover, the diversity of soil fungal communities also increased along the decomposing process of logs. The decaying logs significantly altered soil fungal community composition by affecting biochemical properties (e.g. pH and concentrations of microbial biomass nitrogen and total phosphorus) and environmental factors (e.g. soil water content). Conclusion: Different decay classes of logs favor special fungal species, implying that the logs conservation with different decay classes in the forest ecosystem is of great significance for improving the diversity of soil fungi.

scholarly journals Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9032 ◽  
Author(s):  
Hongjin Liu ◽  
Xinquan Zhao ◽  
Xueping Han ◽  
Shixiao Xu ◽  
Liang Zhao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Species Interactions ◽  
Dry Matter ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
Intestinal Flora ◽  
Tibet Plateau ◽  
Significant Difference ◽  
And Function ◽  
Qinghai Tibet Plateau

Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P < 0.05). No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla Bacteroidetes and Firmicutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than in domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses have advantages over domestic donkeys in dry matter digestion, gut microbial community composition and function, and wild asses have their unique intestinal flora to adapt high altitudes on the Qinghai-Tibet plateau.

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

2020 ◽  
Vol 66 (3) ◽  
pp. 194-205 ◽  
Author(s):  
Fan Chang ◽  
Fengan Jia ◽  
Rui Lv ◽  
Lisha Zhen ◽  
Yan Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Chinese Herb ◽  
Pathogenic Fungi ◽  
Active Phase ◽  
Fungal Communities ◽  
Dynamic Changes ◽  
Metabolic Characteristics ◽  
Herb Residues ◽  
And Function ◽  
Environmental Information Processing

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.

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

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 172 ◽  
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.

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

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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