Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Hui Yao ◽  
Xiang Sun ◽  
Chao He ◽  
Xing-Chun Li ◽  
Liang-Dong Guo
Keyword(s):  
Community Structure ◽  
Endophytic Bacteria ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Network Structures ◽  
Community Structures ◽  
Mangrove Species ◽  
Host Identity ◽  
Biodiversity Maintenance ◽  
Endophytic Bacterial Community

ABSTRACT Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant–epiphytic and plant–endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.

Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China

2020 ◽  
Author(s):  
Yingwu Shi ◽  
Hongmei Yang ◽  
Min Chu ◽  
Xinxiang Niu ◽  
Xiangdong Huo ◽  
...  
Keyword(s):  
Community Structure ◽  
Endophytic Bacteria ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Operational Taxonomic Units ◽  
Cotton Sample ◽  
Endophytic Bacterial Community ◽  
V3 Region ◽  
Illumina Amplicon Sequencing

Endophytic bacteria may be important for plant health and other ecologically relevant functions of cotton. However, the endophytic bacterial community structure and diversity in cotton is still poorly characterized. We investigated the community structure of endophytic bacteria in cotton roots growing in Xinjiang, China, using the Illumina amplicon sequencing. A total of 60.84 M effective sequences of 16S rRNA gene V3 region were obtained from cotton samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in cotton, that is, 81-338 OTUs in a cotton sample, at 3% cutoff level and sequencing depth of 50000 sequences. We identified 23 classes from the resulting 2,723,384 sequences. Gammaproteobacteria were the dominant class in all cottons, followed by Alphaproteobacteria, Actinobacteria and Bacilli. A marked difference in the diversity of endophytic bacteria in cotton for different growth periods was evident. The greatest number of OTUs was detected during seedling (654 OTUs) and budding (381 OTUs). Endophytic bacteria diversity was reduced during flowering (350 OTUs) and boll-opening (351 OTUs). 217 OTUs were common to all four periods. There were more tags of Pantoea in Shihezi than other locations. While there were more tags of Erwinia in Hami than other locations. The dynamics of endophytic bacteria communities were influenced by plant growth stage. These results show the complexity of the bacterial populations present in inner tissues of cotton.

scholarly journals Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Ma ◽  
Geng Wu ◽  
Jian Yang ◽  
Liuqin Huang ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Hydrogen Production ◽  
16S Rrna ◽  
High Throughput Sequencing ◽  
Hot Springs ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

scholarly journals 16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248485
Author(s):  
Edith M. Muwawa ◽  
Chinedu C. Obieze ◽  
Huxley M. Makonde ◽  
Joyce M. Jefwa ◽  
James H. P. Kahindi ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Geographical Location ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Chemical Parameters ◽  
Mangrove Species ◽  
Gazi Bay

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

Endogenous bacterial community structure of Pinus massoniana with differing resistance to pine wilt disease

Nematology ◽  
2021 ◽  
pp. 1-17
Author(s):  
Wei Lu ◽  
Xiao-Jia Zhao ◽  
Jia-Jin Tan
Keyword(s):  
Disease Resistance ◽  
Bacterial Community ◽  
Endophytic Bacteria ◽  
Pine Wilt Disease ◽  
Illumina Miseq ◽  
Pinus Massoniana ◽  
Wilt Disease ◽  
Pine Wilt ◽  
Disease Resistant ◽  
Endophytic Bacterial Community

Summary Pine wilt disease (PWD) is a devastating pine disease caused by Bursaphelenchus xylophilus and its main host in China is Pinus massoniana. The relationship between endophytic bacteria and disease resistance in P. massoniana remains unclear. In this paper, the leaves, roots, stems and treetops of different disease-resistant P. massoniana were studied as the research objective and Illumina MiSeq sequencing was used to analyse whether there were significant differences in the composition and diversity of endophytic bacterial communities between different disease-resistant P. massoniana. The results showed that at the genus level there were no obvious differences in the composition of the endophytic bacterial community of different disease-resistant P. massoniana in the leaves, but there were obvious differences in the roots, stems and treetops. The richness and diversity of endophytic bacteria in P. massoniana had no significant impact on its disease resistance, whilst the structure of endophytic bacterial community in stems and treetops may be related to its disease resistance.

scholarly journals Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

2016 ◽  
Vol 82 (19) ◽  
pp. 5878-5891 ◽  
Author(s):  
Ian M. Bradley ◽  
Ameet J. Pinto ◽  
Jeremy S. Guest
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
Target Genes ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequencing Bias ◽  
Primer Sets

ABSTRACTThe use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3′ end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest.IMPORTANCEThe quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities.

scholarly journals Diversity of Cultivated Endophytic Bacteria from Sugarcane: Genetic and Biochemical Characterization of Burkholderia cepacia Complex Isolates

2007 ◽  
Vol 73 (22) ◽  
pp. 7259-7267 ◽  
Author(s):  
Rodrigo Mendes ◽  
Aline A. Pizzirani-Kleiner ◽  
Welington L. Araujo ◽  
Jos M. Raaijmakers
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Burkholderia Cepacia ◽  
Endophytic Bacteria ◽  
Pathogenic Bacteria ◽  
Biochemical Characterization ◽  
Burkholderia Cepacia Complex ◽  
Rrna Gene ◽  
Endophytic Bacterial Community

ABSTRACT Bacteria were isolated from the rhizosphere and from inside the roots and stems of sugarcane plants grown in the field in Brazil. Endophytic bacteria were found in both the roots and the stems of sugarcane plants, with a significantly higher density in the roots. Many of the cultivated endophytic bacteria were shown to produce the plant growth hormone indoleacetic acid, and this trait was more frequently found among bacteria from the stem. 16S rRNA gene sequence analysis revealed that the selected isolates of the endophytic bacterial community of sugarcane belong to the genera of Burkholderia, Pantoea, Pseudomonas, and Microbacterium. Bacterial isolates belonging to the genus Burkholderia were the most predominant among the endophytic bacteria. Many of the Burkholderia isolates produced the antifungal metabolite pyrrolnitrin, and all were able to grow at 37°C. Phylogenetic analyses of the 16S rRNA gene and recA gene sequences indicated that the endophytic Burkholderia isolates from sugarcane are closely related to clinical isolates of the Burkholderia cepacia complex and clustered with B. cenocepacia (gv. III) isolates from cystic fibrosis patients. These results suggest that isolates of the B. cepacia complex are an integral part of the endophytic bacterial community of sugarcane in Brazil and reinforce the hypothesis that plant-associated environments may act as a niche for putative opportunistic human pathogenic bacteria.

scholarly journals Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Wu ◽  
Fang-Ting Wu ◽  
Qi-Hai Zhou ◽  
Da-Peng Zhao
Keyword(s):  
Community Structure ◽  
Comparative Analysis ◽  
Gut Microbiota ◽  
Species Composition ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Α Diversity ◽  
White Storks

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

scholarly journals The Temporal Structure and Association Networks of Endophytic Bacteria in Pea Roots and Nodules

2021 ◽  
Author(s):  
Xin Lv ◽  
Qiankun Wang ◽  
Xiaoyan Zhang ◽  
Junjie Hao ◽  
Li Li ◽  
...  
Keyword(s):  
Life Cycle ◽  
Bacterial Community ◽  
Endophytic Bacteria ◽  
Developmental Stages ◽  
Temporal Structure ◽  
Mature Stage ◽  
Rrna Gene ◽  
Plant Life ◽  
Endophytic Bacterial Community ◽  
Plant Life Cycle

Abstract Background and aims Endophytic bacteria from legume roots and nodules play important roles in regulating plant growth and health. However, little is known about how the endophytic bacteria community changes and how it interacts with each other throughout the plant life cycle. Methods We collected twenty pea cultivars to study the composition and structure of endophytic bacterial community during the whole developmental period using Illumina sequencing of 16S rRNA gene. Results Here we show that the development period significantly affected the structure of root endophytic bacterial community and peas recruit different root microbes during different developmental stages. The complexity of microbial community first increased and then decreased with the growth of pea. Rhizobium began to accumulate in pea seedling roots, and the content peaked at flowering stage and remained at high levels during the mature stage. In the flowering and mature stage, the relative abundance of Pseudomonas increased. Conclusions These findings can deepen the overall understanding of the community structure and interaction network of endophytic bacteria from pea root and nodules, and provide a detail for the establishment of root endophytic bacteria throughout the plant life cycle.

scholarly journals The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

2020 ◽  
Vol 11 ◽  
Author(s):  
Robin Raveau ◽  
Joël Fontaine ◽  
Mohamed Hijri ◽  
Anissa Lounès-Hadj Sahraoui
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Contaminated Soil ◽  
Mycorrhizal Fungi ◽  
Agricultural Soils ◽  
Illumina Miseq ◽  
Added Value ◽  
Rrna Gene ◽  
Aromatic Plants ◽  
Mycorrhizal Inoculation

To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

scholarly journals Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4970 ◽  
Author(s):  
Ton That Huu Dat ◽  
Georg Steinert ◽  
Nguyen Thi Kim Cuc ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
Coastal Region ◽  
Illumina Miseq ◽  
Sponge Species ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Prokaryotic Diversity ◽  
Class Level ◽  
Wide Range ◽  
Host Identity ◽  
Species Specific

Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylumProteobacteriawas present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast,Chloroflexiwas the most abundant phylum inHalichondriasp., whereasSpirastrellasp. andDactylospongiasp. were dominated byActinobacteria. Several bacterial phyla such asAcidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, andNitrospiraewere found in two-thirds of the sponge species. Moreover, the phylumThaumarchaeota(Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.

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