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

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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Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

PLoS ONE ◽

10.1371/journal.pone.0250675 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250675

Author(s):

Xiang Zheng ◽

Qidi Zhu ◽

Zhijun Zhou ◽

Fangtong Wu ◽

Lixuan Chen ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

Feeding Habits ◽

Bacterial Community Composition ◽

Critical Role ◽

Taxonomic Status ◽

Rrna Gene ◽

Insect Gut

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

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Bacteria associated with jellyfish during bloom and post-bloom periods

10.1101/329524 ◽

2018 ◽

Cited By ~ 1

Author(s):

Maja Kos Kramar ◽

Tinkara Tinta ◽

Davor Lučić ◽

Alenka Malej ◽

Valentina Turk

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Body Part ◽

Body Parts ◽

Population Peak ◽

Significant Difference ◽

Jellyfish Population

AbstractThis study is the first to investigate bacterial community associated with live medusaAurelia sp. in the Gulf of Trieste (northern Adriatic Sea) using both culture independent and culture-based methods. We have analysed bacterial community composition of different body parts of medusa: exumbrella surface, oral arms (‘outer’ body parts) and of gastric cavity (‘inner’ body part) and investigated possible differences in medusa associated bacterial community structure at the time of jellyfish population peak and during senescent phase at the end of bloom, when jellyfish start to decay. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we demonstrated significant difference between bacterial community associated withAureliaand the ambient seawater bacterial assemblage. Comparing bacterial community composition between differentAureliamedusa body parts, communities differed significantly, especially the one within the gastral cavity. The pronounced difference is dominance ofBetaproteobacteria(Burkholderia, CupriavidusandAchromobacter) in gastral cavity of medusa andAlpha- (Phaeobacter, Ruegeria) andGamma-proteobacteria(Stenotrophomonas, Alteromonas, PseudoalteromonasandVibrio) on ‘outer’ body parts. This suggests that body-part specific bacterial association might have an important functional roles for the host. The results of bacterial isolates showed the dominance ofGammaproeteobacteria, especiallyVibrioandPseudoalteromonasin all body parts. Finally, comparison of medusa associated bacterial community structure, at the time of jellyfish population peak and during senescent phase at the end of bloom showed increased abundance ofGammaproteobacteria, especiallyVibrio. Our results suggest members ofVibriogroup are possible commensal opportunistic visitors, later becoming consumer of moribund jellyfish biomass and that the structure of jellyfish bacterial community might be affected by anthropogenic pollution in the marine environment.

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Effect of Sheep Urine Deposition on the Bacterial Community Structure in an Acidic Upland Grassland Soil

Applied and Environmental Microbiology ◽

10.1128/aem.00926-06 ◽

2006 ◽

Vol 72 (11) ◽

pp. 7231-7237 ◽

Cited By ~ 21

Author(s):

Deirdre Rooney ◽

Nabla Kennedy ◽

Louise Deering ◽

Deirdre Gleeson ◽

Nicholas Clipson

Keyword(s):

Community Structure ◽

Microbial Biomass ◽

Bacterial Community ◽

Microbial Activity ◽

Community Composition ◽

Plant Species ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

High Concentrations ◽

Sheep Urine

ABSTRACT The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.

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Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams

Applied and Environmental Microbiology ◽

10.1128/aem.01715-10 ◽

2010 ◽

Vol 77 (1) ◽

pp. 302-311 ◽

Cited By ~ 93

Author(s):

Tatiana A. Vishnivetskaya ◽

Jennifer J. Mosher ◽

Anthony V. Palumbo ◽

Zamin K. Yang ◽

Mircea Podar ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Inorganic Mercury ◽

Rrna Gene ◽

Oak Ridge

ABSTRACTHigh concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, includingProteobacteria(ranging from 22.9 to 58.5% per sample),Cyanobacteria(0.2 to 32.0%),Acidobacteria(1.6 to 30.6%),Verrucomicrobia(3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within theProteobacteriagroup that includes sulfate-reducing bacteria and within theVerrucomicrobiagroup appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on thein situmicrobial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.

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Divergence in Gut Bacterial Community Among Life Stages of the Rainbow Stag Beetle Phalacrognathus muelleri (Coleptera: Lucanidae)

Insects ◽

10.3390/insects11100719 ◽

2020 ◽

Vol 11 (10) ◽

pp. 719

Author(s):

Miaomiao Wang ◽

Xingjia Xiang ◽

Xia Wan

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Illumina Miseq ◽

Life Stages ◽

Early Instar

Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community.

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Effects of Chemical and Solar Soil-Disinfection Methods on Soil Bacterial Communities

Sustainability ◽

10.3390/su12239833 ◽

2020 ◽

Vol 12 (23) ◽

pp. 9833

Author(s):

Cuixia Yun ◽

Enke Liu ◽

Massimo Rippa ◽

Pasquale Mormile ◽

Dongbao Sun ◽

...

Keyword(s):

Activated Carbon ◽

Community Structure ◽

Solar Radiation ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Disinfection Methods ◽

Soil Disinfection ◽

Soil Bacterial

The actctivated carbon + solar radiation membrane is an eco-friendly soil disinfestations method for managing soil-borne plant pathogens. However, little was known the impact of Activated carbon + solar radiation membrane on bacterial community structure in strawberry production systems under field conditions. A comprehensive evaluation of the impacts of different soil disinfection methods on the bacterial community structure is fundamental to understand the role of disinfection in maintaining soil health. The changes in the soil bacterial diversity and community composition were detected using realtime fluorescence quantitative PCR (RTFQ PCR) and next-generation sequencing techniques to better understand the effect of soil disinfection. The bacterial community composition was monitored after disinfection using dazomet (DZ), chloropicrin (CP), 100 kg/ha activated carbon + solar radiation membrane (AC1), 200 kg/ha activated carbon + solar radiation membrane (AC2), and 300 kg/ha activated carbon + solar radiation membrane (AC3) and compared with the control (CT). The results indicated that the different dosages of activated carbon (AC1, AC2, and AC3) did not affect the bacterial community structure. On the other hand, DZ and CP considerably reduced the soil biomass and abundance of bacterial species. Chemical fumigants influenced the bacterial community structure, with DZ treatment leading to the dominance of the phylum Firmicutes, accounting for approximately 54%. After fumigation with CP, Proteobacteria and Acidobacteria were the dominant phyla. Beta diversity analysis and principal coordinate analysis revealed that the bacterial communities in the soil treated with DZ and CP formed clusters. Redundancy analysis indicated that soil pH, available potassium, and available phosphorus were the key factors influencing microbial metabolic functional diversity. Thus, it was verified that the damage caused by activated carbon + solar radiation membrane—a potential alternative for chemical fumigant—to the soil bacterial community was less than that caused by chemicals DZ and CP.

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Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽

10.3390/w13111465 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1465

Author(s):

Chao Shen ◽

Liuyan Huang ◽

Guangwu Xie ◽

Yulai Wang ◽

Zongkai Ma ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Diversity Index ◽

Plastic Substrate ◽

Simpson Index ◽

Plastic Debris ◽

Plastic Substrates ◽

Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

Author(s):

Christian L. Lauber ◽

Micah Hamady ◽

Rob Knight ◽

Noah Fierer

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Spatial Scales ◽

Bacterial Community Composition ◽

Phylogenetic Structure ◽

Soil Bacterial Communities ◽

Soil Bacterial Community Structure ◽

Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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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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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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