Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca

Abstract Background Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. Results A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). Conclusion The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

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Insights into the Endophytic Bacterial Community Comparison and their Potential Role in the Dimorphic Seeds of Halophyte Suaeda Glauca

10.21203/rs.3.rs-153202/v1 ◽

2021 ◽

Author(s):

Hongfei Wang ◽

Manik Prabhu Narsing Rao ◽

Yanli Gao ◽

Xinyang Li ◽

Rui Gao ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Seed Coat ◽

Bacterial Communities ◽

Endophytic Bacteria ◽

Ecological Adaptation ◽

Endophytic Bacterial Community ◽

Suaeda Glauca ◽

Black Seeds ◽

Disturbed Environment

Abstract Background: The seed dimorphism was thought to be a bet-hedging strategy, which assists plants to survive in the disturbed environment and has been widely studied for their ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In the present study, we firstly used 16S rRNA high-throughput gene sequencing method to compare the bacterial diversity and community composition between brown and black seeds of Suaeda glauca. Results: A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e. pectinase, cellulolytic and xylanolytic activities). Conclusion: The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different bacterial function roles. The endophytic bacterial communities of the dimorphic seeds might be influenced mainly by the seed coat structure and partly by seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

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Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China

Microorganisms ◽

10.3390/microorganisms7020047 ◽

2019 ◽

Vol 7 (2) ◽

pp. 47 ◽

Cited By ~ 6

Author(s):

Zhen-Shan Deng ◽

Bao-Cheng Zhang ◽

Xiang-Ying Qi ◽

Zhi-Hong Sun ◽

Xiao-Long He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Endophytic Bacteria ◽

Growth Promotion ◽

Bacterial Community Composition ◽

Shannon Index ◽

Plant Production ◽

Total Carbon ◽

Shaanxi Province ◽

Endophytic Bacterial Community

Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.

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Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽

10.7717/peerj.5508 ◽

2018 ◽

Vol 6 ◽

pp. e5508 ◽

Cited By ~ 3

Author(s):

Yan Li ◽

Yan Kong ◽

Dexiong Teng ◽

Xueni Zhang ◽

Xuemin He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Community Diversity ◽

Species Identity ◽

Halostachys Caspica ◽

Lycium Ruthenicum ◽

Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

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Diversity Analysis of Endophytic Bacterial Community in Two Citrus Cultivars With Different Resistance to Citrus Canker

10.21203/rs.3.rs-347972/v1 ◽

2021 ◽

Author(s):

Bing Liu ◽

Jiahao Lai ◽

Simeng Wu ◽

Junxi Jiang ◽

Weigang Kuang

Keyword(s):

Bacterial Community ◽

Endophytic Bacteria ◽

Citrus Canker ◽

Navel Orange ◽

Xanthomonas Citri ◽

Canker Disease ◽

Satsuma Mandarin ◽

Endophytic Bacterial Community ◽

Dominant Bacteria ◽

The Relationship

Abstract The selective infection of Xanthomonas citri pv. citri to citrus cultivars is universally known, but it is not clarified whether there is a relationship between endophytic bacteria and the resistance of host variety to canker disease. In order to explore the relationship, Satsuma mandarin and Newhall navel orange were collected respectively as samples of resistant or susceptible cultivars to citrus canker disease, and endophytic bacterial community of two citrus cultivars were analyzed by using a next-generation, Illumina-based sequencing approach. Simultaneously, the seasonal dynamics of endophytic bacterial community and dominant genera were analyzed. The results showed that there were four dominant groups including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes in all samples at phylum level. Endophytic bacteria were the most abundant in spring samples, then in summer and autumn samples. There were some differences between endophytic bacterial community of resistant citrus and that of susceptible citrus to canker disease, and the endophytic bacteria of Satsuma mandarin are more abundant than that of Newhall navel orange. According to the analysis of dominant bacteria in two citrus cultivars, it was found that some endophytic bacteria with antagonistic characteristics existed universally in all samples, although the dominant bacteria in different seasonal sample were different. However, in Newhall navel orange of susceptible citrus to canker disease, there were not only some bacteria against Xanthomonas citri pv. citri, but also some cooperative bacteria of canker occurrence like Stenotrophomonas.

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Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

Scientific Reports ◽

10.1038/s41598-020-66638-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mayank Krishna ◽

Shruti Gupta ◽

Manuel Delgado – Baquerizo ◽

Elly Morriën ◽

Satish Chandra Garkoti ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Secondary Succession ◽

Positive Association ◽

Ecological Networks ◽

Growth Stages ◽

Ecosystem Recovery ◽

Soil Bacterial

Abstract This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

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Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽

10.3390/ani10040701 ◽

2020 ◽

Vol 10 (4) ◽

pp. 701 ◽

Cited By ~ 1

Author(s):

Fengling Zhang ◽

Xingjia Xiang ◽

Yuanqiu Dong ◽

Shaofei Yan ◽

Yunwei Song ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Stopover Site ◽

Intestinal Bacterial Community ◽

Hooded Crane ◽

Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

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Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea

Microorganisms ◽

10.3390/microorganisms7100385 ◽

2019 ◽

Vol 7 (10) ◽

pp. 385

Author(s):

Yunyun Fu ◽

Richard B. Rivkin ◽

Andrew S. Lang

Keyword(s):

Bacterial Community ◽

Sea Ice ◽

Arctic Ocean ◽

Community Composition ◽

Bacterial Communities ◽

Water Mass ◽

Beaufort Sea ◽

The Arctic ◽

The Arctic Ocean ◽

Mass Segregation

The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance.

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Multiple Stressors Determine Community Structure and Estimated Function of River Biofilm Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.00291-20 ◽

2020 ◽

Vol 86 (12) ◽

Cited By ~ 1

Author(s):

Ferran Romero ◽

Vicenç Acuña ◽

Sergi Sabater

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Pesticide Exposure ◽

Multiple Stressors ◽

Bacterial Community Composition ◽

Freshwater Ecosystems ◽

Low Flow ◽

Hydrological Stress ◽

The Individual

ABSTRACT Freshwater ecosystems are exposed to multiple stressors, but their individual and combined effects remain largely unexplored. Here, we investigated the response of stream biofilm bacterial communities to warming, hydrological stress, and pesticide exposure. We used 24 artificial streams on which epilithic (growing on coarse sediments) and epipsammic (growing on fine sediments) stream biofilms were maintained. Bacterial community composition and estimated function of biofilms exposed during 30 days to individual and combined stressors were assessed using 16S rRNA gene metabarcoding. Among the individual effects by stressors, hydrological stress (i.e., a simulated low-flow situation) was the most relevant, since it significantly altered 57% of the most abundant bacterial taxa (n = 28), followed by warming (21%) and pesticide exposure (11%). Regarding the combined effects, 16% of all stressor combinations resulted in significant interactions on bacterial community composition and estimated function. Antagonistic responses prevailed (57 to 89% of all significant interactions), followed by synergisms (11 to 43%), on specific bacterial taxa, indicating that multiple-stressor scenarios could lead to unexpected shifts in the community composition and associated functions of riverine bacterial communities. IMPORTANCE Freshwater ecosystems such as rivers are of crucial importance for human well-being. However, human activities result in many stressors (e.g., toxic chemicals, increased water temperatures, and hydrological alterations) cooccurring in rivers and streams worldwide. Among the many organisms inhabiting rivers and streams, bacteria are ecologically crucial; they are placed at the base of virtually all food webs and they recycle the organic matter needed for bigger organisms. Most of these bacteria are in close contact with river substratum, where they form the biofilms. There is an urgent need to evaluate the effects of these stressors on river biofilms, so we can anticipate future environmental problems. In this study, we experimentally exposed river biofilms to a pesticide mixture, an increase in water temperature and a simulated low-flow condition, in order to evaluate the individual and joint effects of these stressors on the bacterial community composition and estimated function.

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Changes in Free-Living and Particle-Associated Bacterial Communities Depending on the Growth Phases of Marine Green Algae, Tetraselmis suecica

Journal of Marine Science and Engineering ◽

10.3390/jmse9020171 ◽

2021 ◽

Vol 9 (2) ◽

pp. 171

Author(s):

Bum Soo Park ◽

Won-Ji Choi ◽

Ruoyu Guo ◽

Hansol Kim ◽

Jang-Seu Ki

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Green Algae ◽

Growth Phase ◽

Bacterial Communities ◽

Algal Growth ◽

Cell Number ◽

Phase Lag ◽

Tetraselmis Suecica ◽

Free Living

Bacteria are remarkably associated with the growth of green algae Tetraselmis which are used as a feed source in aquaculture, but Tetraselmis-associated bacterial community is characterized insufficiently. Here, as a first step towards characterization of the associated bacteria, we investigated the community composition of free-living (FLB) and particle-associated (PAB) bacteria in each growth phase (lag, exponential, stationary, and death) of Tetraselmis suecica P039 culture using pyrosequencing. The percentage of shared operational taxonomic units (OTUs) between FLB and PAB communities was substantially high (≥92.4%), but their bacterial community compositions were significantly (p = 0.05) different from each other. The PAB community was more variable than the FLB community depending on the growth phase of T. suecica. In the PAB community, the proportions of Marinobacter and Flavobacteriaceae were considerably varied in accordance with the cell number of T. suecica, but there was no clear variation in the FLB community composition. This suggests that the PAB community may have a stronger association with the algal growth than the FLB community. Interestingly, irrespective of the growth phase, Roseobacter clade and genus Muricauda were predominant in both FLB and PAB communities, indicating that bacterial communities in T. suecica culture may positively affect the algae growth and that they are potentially capable of enhancing the T. suecica growth.

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Variation of bacterial communities in Muztagh ice core from 1869 to 2000

10.5194/egusphere-egu2020-6328 ◽

2020 ◽

Author(s):

Yongqin Liu ◽

Tandong Yao ◽

Baiqing Xu

Keyword(s):

Bacterial Community ◽

Temporal Variation ◽

Community Composition ◽

Bacterial Communities ◽

Environmental Variables ◽

Climate Changes ◽

Bacterial Community Composition ◽

Ice Core ◽

The Past ◽

Stage 1

Many studies focusing on the physical and chemical indicators of the ice core reflected the climate changes. However, only few biological indicators indicated the past climate changes which are mainly focused in biomass rather than diversity. How the biodiversity response to the climate change during the past hundred years is still unknow. Glaciers in Mt. Muztagh Ata region are in&#64258;uenced by the year-round westerly circulation. We firstly disclosed annual variations of bacterial community compositions in ice core over the past 130 years from Muztagh Glacier, the western Tibetan Plateau. Temporal variation in bacterial abundance was strongly controlled by DOC, TN, &#948;18O, Ca2+, SO42&#8722;, NH4+ and NO3&#8722;. Proteobacteria, Actinobacteria and Firmicutes were the three most abundant bacterial phyla, accounting for 49.3%, 21.3% and 11.0% of the total community, respectively. The abundances of Firmicutes and Bacteroidetes pronouncedly increased over time throughout the entire ice core. UPGMA cluster analysis of the bacterial community composition separated the all ice core samples into two main clusters along the temporal variation. The first cluster consisted of samples from 1951 to 2000 and the second cluster contained main samples during the period of 1869-1950. The stage 1 and stage 2 bacterial community dissimilarities increased linearly with time on the basis of the Bray-Curtis distance, indicating a similar temporal&#8211;decay relationship between the stage 1 and stage 2 bacterial communities. Of all the environmental variables examined, only DOC and NH4+ exhibited very strong negative correlations with bacterial Chao1-richness. 18O was another important variable in shaping the ice core bacterial community composition and contributed 1.6% of the total variation. Moreover, DistLM analysis indicated that the environmental variables explained more variation in the stage 1 community (20.1%) than that of the stage 2 community (19.9%).

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