Journal articles: 'Bacterial communities'

1

Tetz, V. V., V. P. Korobov, N. K. Artemenko, L. M. Lemkina, N. V. Panjkova, and G. V. Tetz. "Extracellular phospholipids of isolated bacterial communities." Biofilms 1, no. 3 (July 2004): 149–55. http://dx.doi.org/10.1017/s147905050400136x.

Full text

Abstract:

We have made a comparative analysis of the extracellular phospholipid composition of biofilms of Gram-negative and Gram-positive bacteria. The surface film of a growing bacterial community contains small membrane vesicles and a bilipid layer covering the entire surface of that community. These supracommunity films containing the bilipid layer can cover the entire surface of a Petri dish and form a boundary between bacterial communities and the environment. A mixed bacterial lawn, formed by unrelated bacteria, also becomes covered with a single film containing a lipid bilayer. The phospholipid compositions of the bacterial cell and surface film bilipid layer reflect the nature of the bacterial strains forming the community, but have some specific differences.

APA, Harvard, Vancouver, ISO, and other styles

2

Karim, Md Abdul, and Mehedi Al Masum. "Characteristics and antibiogram of airborne bacterial communities." Bangladesh Journal of Botany 49, no. 4 (December 31, 2020): 937–47. http://dx.doi.org/10.3329/bjb.v49i4.52501.

Full text

Abstract:

Composition and concentration of the bacterial communities in air of using a culture-dependent plate exposure technique and air sampling with filter were analysed. An average value of 2.8 x 103 bacterial CFU/m3 was found in different seasons. A total of 8 bacterial genera were identified among 58 species. The most predominant bacteria were Bacillus (73%), Planococcus (9%), Staphylococcus (6%), Micrococcus (4%), Deinococcus (2%), Arthrobacter (2%), Microbacterium (2%), and Exiguobacterium (2%). The distribution of predominant airborne bacteria varied greatly between different sampling sites and seasons and was limited by environmental parameters, as well as human activities.

APA, Harvard, Vancouver, ISO, and other styles

3

He, Ping-An, and Li Xia. "Oligonucleotide Profiling for Discriminating Bacteria in Bacterial Communities." Combinatorial Chemistry & High Throughput Screening 10, no. 4 (May 1, 2007): 247–55. http://dx.doi.org/10.2174/138620707780636646.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

Harcombe, W. R., and J. J. Bull. "Impact of Phages on Two-Species Bacterial Communities." Applied and Environmental Microbiology 71, no. 9 (September 2005): 5254–59. http://dx.doi.org/10.1128/aem.71.9.5254-5259.2005.

Full text

Abstract:

ABSTRACT A long history of experimental work has shown that addition of bacteriophages to a monoculture of bacteria leads to only a temporary depression of bacterial levels. Resistant bacteria usually become abundant, despite reduced growth rates relative to those of phage-sensitive bacteria. This restoration of high bacterial density occurs even if the phages evolve to overcome bacterial resistance. We believe that the generality of this result may be limited to monocultures, in which the resistant bacteria do not face competition from bacterial species unaffected by the phage. As a simple case, we investigated the impact of phages attacking one species in a two-species culture of bacteria. In the absence of phages, Escherichia coli B and Salmonella enterica serovar Typhimurium were stably maintained during daily serial passage in glucose minimal medium (M9). When either of two E. coli-specific phages (T7 or T5) was added to the mixed culture, E. coli became extinct or was maintained at densities that were orders of magnitude lower than those before phage introduction, even though the E. coli densities with phage reached high levels when Salmonella was absent. In contrast, the addition of a phage that attacked only Salmonella (SP6) led to transient decreases in the bacterial number whether E. coli was absent or present. These results suggest that phages can sometimes, although not always, provide long-term suppression of target bacteria.

APA, Harvard, Vancouver, ISO, and other styles

5

Stephens, Colton R. A., Breanne M. McAmmond, Jonathan D. Van Hamme, Ken A. Otter, Matthew W. Reudink, and Eric M. Bottos. "Analysis of bacterial communities associated with Mountain Chickadees (Poecile gambeli) across urban and rural habitats." Canadian Journal of Microbiology 67, no. 8 (August 2021): 572–83. http://dx.doi.org/10.1139/cjm-2020-0320.

Full text

Abstract:

Host-associated microbial communities play important roles in wildlife health, but these dynamics can be influenced by environmental factors. Urbanization has numerous effects on wildlife; however, the degree to which wildlife-associated bacterial communities and potential bacterial pathogens vary across urban–rural/native habitat gradients remains largely unknown. We used 16S rRNA gene amplicon sequencing to examine bacterial communities found on Mountain Chickadee (Poecile gambeli) feathers and nests in urban and rural habitats. The feathers and nests in urban and rural sites had similar abundances of major bacterial phyla and dominant genera with pathogenic members. However, richness of bacterial communities and potential pathogens on birds were higher in urban habitats, and potential pathogens accounted for some of the differences in bacterial occurrence between urban and rural environments. We predicted habitat using potential pathogen occurrence with a 90% success rate for feather bacteria, and a 72.2% success rate for nest bacteria, suggesting an influence of urban environments on the presence of potential pathogens. We additionally observed similarities in bacterial communities between nests and their occupants, suggesting bacterial transmission between them. These findings improve our understanding of the bacterial communities associated with urban wildlife and suggest that urbanization impacts the composition of wildlife-associated bacterial communities.

APA, Harvard, Vancouver, ISO, and other styles

6

Dionisio, Francisco, Ivan Matic, Miroslav Radman, Olivia R. Rodrigues, and François Taddei. "Plasmids Spread Very Fast in Heterogeneous Bacterial Communities." Genetics 162, no. 4 (December 1, 2002): 1525–32. http://dx.doi.org/10.1093/genetics/162.4.1525.

Full text

Abstract:

Abstract Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This “amplification effect” could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes.

APA, Harvard, Vancouver, ISO, and other styles

7

Montalvo, Naomi F., and Russell T. Hill. "Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts." Applied and Environmental Microbiology 77, no. 20 (August 19, 2011): 7207–16. http://dx.doi.org/10.1128/aem.05285-11.

Full text

Abstract:

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

APA, Harvard, Vancouver, ISO, and other styles

8

Wade, W. G., and E. M. Prosdocimi. "Profiling of Oral Bacterial Communities." Journal of Dental Research 99, no. 6 (April 14, 2020): 621–29. http://dx.doi.org/10.1177/0022034520914594.

Full text

Abstract:

The profiling of bacterial communities by the sequencing of housekeeping genes such as that encoding the small subunit ribosomal RNA has revealed the extensive diversity of bacterial life on earth. Standard protocols have been developed and are widely used for this application, but individual habitats may require modification of methods. This review discusses the sequencing and analysis methods most appropriate for the study of the bacterial component of the human oral microbiota. If possible, DNA should be extracted from samples soon after collection. If samples have to be stored for practical reasons, precautions to avoid DNA degradation on freezing should be taken. A critical aspect of profiling oral bacterial communities is the choice of region of the 16S rRNA gene for sequencing. The V1-V2 region provides the best discrimination between species of the genus Streptococcus, the most common genus in the mouth and important in health and disease. The MiSeq platform is most commonly used for sequencing, but long-read technologies are now becoming available that should improve the resolution of analyses. There are a variety of well-established data analysis pipelines available, including mothur and QIIME, which identify sequence reads as phylotypes by comparing them to reference data sets or grouping them into operational taxonomic units. DADA2 has improved sequence error correction capabilities and resolves reads to unique variants. Two curated oral 16S rRNA databases are available: HOMD and CORE. Expert interpretation of community profiles is required, both to detect the presence of contaminating DNA, which is commonly present in the reagents used in analysis, and to differentiate oral and nonoral bacteria and determine the significance of findings. Despite advances in shotgun whole-genome metagenomic methods, oral bacterial community profiling via 16S rRNA sequence analysis remains a valuable technique for the characterization of oral bacterial populations.

APA, Harvard, Vancouver, ISO, and other styles

9

Bates, Scott T., Garrett W. G. Cropsey, J. Gregory Caporaso, Rob Knight, and Noah Fierer. "Bacterial Communities Associated with the Lichen Symbiosis." Applied and Environmental Microbiology 77, no. 4 (December 17, 2010): 1309–14. http://dx.doi.org/10.1128/aem.02257-10.

Full text

Abstract:

ABSTRACTLichens are commonly described as a mutualistic symbiosis between fungi and “algae” (ChlorophytaorCyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated byAlphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associatedRhizobialeslineage (LAR1; putative N2fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2fixers (e.g.,Azospirillum,Bradyrhizobium, andFrankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

APA, Harvard, Vancouver, ISO, and other styles

10

Guo, Yufang. "Bacterial communities by design." Nature Food 3, no. 5 (May 2022): 303. http://dx.doi.org/10.1038/s43016-022-00527-6.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Deepika, Sandhya, and K. Laxmi Sowmya. "Bioindices of Bacterial Communities." International Journal of Current Microbiology and Applied Sciences 5, no. 12 (December 10, 2016): 219–33. http://dx.doi.org/10.20546/ijcmas.2016.512.024.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Ostovar, Ghazaleh, Kyle L. Naughton, and James Q. Boedicker. "Computation in bacterial communities." Physical Biology 17, no. 6 (October 9, 2020): 061002. http://dx.doi.org/10.1088/1478-3975/abb257.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Weitzman, Chava L., Karen Gibb, and Keith Christian. "Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia." PeerJ 6 (November 14, 2018): e5960. http://dx.doi.org/10.7717/peerj.5960.

Full text

Abstract:

Animal skin acts as a barrier between the organism and its environment and provides the first line of defense against invading pathogens. Thus, skin surfaces harbor communities of microbes that are interacting with both the host and its environment. Amphibian skin bacteria form distinct communities closely tied to their host species, but few studies have compared bacterial communities between amphibians and other, non-amphibian sympatric animals. Notably, skin microbes on reptiles have gained little attention. We used next-generation sequencing technology to describe bacterial communities on the skin of three lizard species and compared them to bacteria on six cohabiting frog species in the Northern Territory of Australia. We found bacterial communities had higher richness and diversity on lizards than frogs, with different community composition between reptiles and amphibians and among species. Core bacteria on the three lizard species overlapped by over 100 operational taxonomic units. The bacterial communities were similar within species of frogs and lizards, but the communities tended to be more similar between lizard species than between frog species and when comparing lizards with frogs. The diverse bacteria found on lizards invites further questions on how and how well reptiles interact with microorganisms through their scaly skin.

APA, Harvard, Vancouver, ISO, and other styles

14

Gasol, Josep M., and Paul A. Del Giorgio. "Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities." Scientia Marina 64, no. 2 (June 30, 2000): 197–224. http://dx.doi.org/10.3989/scimar.2000.64n2197.

Full text

APA, Harvard, Vancouver, ISO, and other styles

15

Jones, Ryan T., Alberto Bressan, April M. Greenwell, and Noah Fierer. "Bacterial Communities of Two Parthenogenetic Aphid Species Cocolonizing Two Host Plants across the Hawaiian Islands." Applied and Environmental Microbiology 77, no. 23 (September 30, 2011): 8345–49. http://dx.doi.org/10.1128/aem.05974-11.

Full text

Abstract:

ABSTRACTAphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid,Aphis gossypii, and the cardamom aphid,Pentalonia caladii) cocolonizing two plant species (taro,Colocasia esculenta, and ginger,Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, andA. gossypiiharbored a more diverse bacterial community thanP. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants.

APA, Harvard, Vancouver, ISO, and other styles

16

Salam, Md Tareq Bin, and Ryota Kataoka. "Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides." International Journal of Molecular Sciences 24, no. 20 (October 18, 2023): 15306. http://dx.doi.org/10.3390/ijms242015306.

Full text

Abstract:

Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.

APA, Harvard, Vancouver, ISO, and other styles

17

Hospodsky, Denina, Amy J. Pickering, Timothy R. Julian, Dana Miller, Sisira Gorthala, Alexandria B. Boehm, and Jordan Peccia. "Hand bacterial communities vary across two different human populations." Microbiology 160, no. 6 (June 1, 2014): 1144–52. http://dx.doi.org/10.1099/mic.0.075390-0.

Full text

Abstract:

This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of US women. Bacterial population profiles and phylogenetically based ordinate analysis demonstrated that the bacterial communities on hands were more similar for selected populations within a country than between the two countries considered. Organisms that have commonly been identified in prior human skin microbiome studies, including members of the Propionibacteriaceae, Staphylococcaceae and Streptococceacea families, were highly abundant on US hands and drove the clustering of US hand microbial communities into a distinct group. The most abundant bacterial taxa on Tanzanian hands were the soil-associated Rhodobacteraceae and Nocardioidaceae. These results help to expand human microbiome results beyond US and European populations, and the identification and abundance of soil-associated bacteria on Tanzanian hands demonstrated the important role of the environment in shaping the microbial communities on human hands.

APA, Harvard, Vancouver, ISO, and other styles

18

Bi, Siyan, Xiaodi Wang, Yanhong Tang, Kexin Lei, Jianyang Guo, Nianwan Yang, Fanghao Wan, Zhichuang Lü, and Wanxue Liu. "Bacterial Communities of the Internal Reproductive and Digestive Tracts of Virgin and Mated Tuta absoluta." Insects 14, no. 10 (September 22, 2023): 779. http://dx.doi.org/10.3390/insects14100779.

Full text

Abstract:

Microorganisms can affect host reproduction, defense, and immunity through sexual or opportunistic transmission; however, there are few studies on insect reproductive organs and intestinal bacterial communities and their effects on mating. Tuta absoluta is a worldwide quarantine pest that seriously threatens the production of Solanaceae crops, and the microbial community within tomato leafminers remains unclear. In this study, 16s rRNA sequencing was used to analyze bacterial communities related to the reproductive organs and intestinal tracts of tomato leafminers (the sample accession numbers are from CNS0856533 to CNS0856577). Different bacterial communities were found in the reproductive organs and intestinal tracts of females and males. Community ecological analysis revealed three potential signs of bacterial sexual transmission: (1) Mating increased the similarity between male and female sex organs and intestinal communities. (2) The bacteria carried by mated individuals were found in unmated individuals of the opposite sex but not in unmated individuals of the same sex. (3) The bacteria carried by unmated individuals were lost after mating. In addition, the abundances of bacterial communities carried by eggs were significantly higher than those of adult worms. Our results confirm that mating leads to the transfer of bacterial communities in the reproductive organs and gut of tomato leafminers, and suggest that this community strongly influences the reproductive process.

APA, Harvard, Vancouver, ISO, and other styles

19

XG, Zhou, Wu FZ, and Xiang WS. "Syringic acid inhibited cucumber seedling growth and changed rhizosphere microbial communities." Plant, Soil and Environment 60, No. 4 (April 8, 2014): 158–64. http://dx.doi.org/10.17221/924/2013-pse.

Full text

Abstract:

Phenolic compounds enter soil as a result of root exudation and plant residue decomposition, but their impacts on soil microbial communities are poorly understood. In this experiment, effects of syringic acid on cucumber rhizosphere microbial communities were evaluated. Rhizosphere bacterial and fungal community structures and abundances were analyzed with PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR, respectively. Results showed that syringic acid inhibited cucumber seedling growth at concentrations of 0.05 to 0.2 μmol/g soil, and increased rhizosphere soil dehydrogenase activity, microbial biomass carbon content, bacterial 16S rRNA gene and fungal ITS rRNA gene densities, and decreased the bacteria-to-fungi ratio at concentrations of 0.02 to 0.2 μmol/g soil. Syringic acid also changed rhizosphere bacterial and fungal community structures: it decreased the richness, evenness, and diversity indices of rhizosphere bacterial community but had no significant influences on that of fungal community, indicating that syringic acid had different influence on bacterial and fungal communities. Taken together, these results showed that syringic acid inhibited cucumber growth and altered rhizosphere microbial communities, suggesting that syringic acid plays some role in the communication between plants and soil microorganisms.

APA, Harvard, Vancouver, ISO, and other styles

20

Xia, Xiaomin, Jianjun Wang, Jiabin Ji, Jiexia Zhang, Liqi Chen, and Rui Zhang. "Bacterial Communities in Marine Aerosols Revealed by 454 Pyrosequencing of the 16S rRNA Gene*." Journal of the Atmospheric Sciences 72, no. 8 (August 1, 2015): 2997–3008. http://dx.doi.org/10.1175/jas-d-15-0008.1.

Full text

Abstract:

Abstract Although bacteria are an important biological component of aerosol particles, studies of bacterial communities in remote marine aerosol are largely lacking. In this study, aerosol samples were collected over the western Pacific Ocean, the northern Pacific Ocean, the Arctic Ocean, and the Norwegian Sea during the Fifth Chinese National Arctic Research Expedition (CHINARE 5). The diversity and structure of aerosol bacterial communities, based on 454 pyrosequencing, were explored in these samples. The bacterial community in the aerosols collected over the Pacific Ocean was more diverse than over the Norwegian Sea. Both temporal and spatial variations in aerosol bacterial communities were observed based on phylogenetic analysis. These results suggest that the source of air masses shape bacterial communities in aerosol particles over remote marine regions. Aerosols are clearly important for long-range transport of bacteria. Since potential human pathogens (e.g., Streptococcus sp.) were retrieved in this study, further investigation is needed to evaluate the potential for their long-distance migration via aerosol.

APA, Harvard, Vancouver, ISO, and other styles

21

Villegas, Luis E. Martinez, James Radl, George Dimopoulos, and Sarah M. Short. "Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues." PLOS Neglected Tropical Diseases 17, no. 3 (March 29, 2023): e0011218. http://dx.doi.org/10.1371/journal.pntd.0011218.

Full text

Abstract:

Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, other compartments of the digestive tract maintain communities of bacteria which remain almost entirely unstudied. For example, the Dipteran crop is a food storage organ, but few studies have looked at the microbiome of crops in mosquitoes, and only a single previous study has investigated the crop in Ae. aegypti. In this study, we used both culture-dependent and culture-independent methods to compare the bacterial communities in midguts and crops of laboratory reared Ae. aegypti. Both methods revealed a trend towards higher abundance, but also higher variability, of bacteria in the midgut than the crop. When present, bacteria from the genus Elizabethkingia (family Weeksellaceae) dominated midgut bacterial communities. In crops, we found a higher diversity of bacteria, and these communities were generally dominated by acetic acid bacteria (family Acetobacteriaceae) from the genera Tanticharoenia and Asaia. These three taxa drove significant community structure differences between the tissues. We used FAPROTAX to predict the metabolic functions of these communities and found that crop bacterial communities were significantly more likely to contain bacteria capable of methanol oxidation and methylotrophy. Both the presence of acetic acid bacteria (which commonly catabolize sugar to produce acetic acid) and the functional profile that includes methanol oxidation (which is correlated with bacteria found with natural sources like nectar) may relate to the presence of sugar, which is stored in the mosquito crop. A better understanding of what bacteria are present in the digestive tract of mosquitoes and how these communities assemble will inform how the microbiota impacts mosquito physiology and the full spectrum of functions provided by the microbiota. It may also facilitate better methods of engineering the mosquito microbiome for vector control or prevention of disease transmission.

APA, Harvard, Vancouver, ISO, and other styles

22

Djokic, Lidija, M. Savic, Tanja Narancic, and Branka Vasiljevic. "Metagenomic analysis of soil microbial communities." Archives of Biological Sciences 62, no. 3 (2010): 559–64. http://dx.doi.org/10.2298/abs1003559d.

Full text

Abstract:

Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity. .

APA, Harvard, Vancouver, ISO, and other styles

23

Yuan, Zong-sheng, Fang Liu, Shi-bin He, Li-li Zhou, and Hui Pan. "Community structure and diversity characteristics of rhizosphere and root endophytic bacterial community in different Acacia species." PLOS ONE 17, no. 1 (January 31, 2022): e0262909. http://dx.doi.org/10.1371/journal.pone.0262909.

Full text

Abstract:

Rhizosphere and endophytic microbiota significantly affect plant growth and development by influencing nutrient uptake and stress tolerance. Herein, root and rhizosphere soil of Acacia species were collected and analyzed to compare the structural differences of the rhizosphere and root endophytic bacterial communities. High-throughput 16S rRNA gene sequencing technology was employed to analyze the rhizosphere and root endophytic bacterial communities. A total of 4249 OTUs were identified following sequence analysis. The rhizosphere soil contained significantly more OTUs than the root soil. Principal component analysis (PCA) and hierarchical cluster analysis indicated that bacterial communities exhibited significant specificity in the rhizosphere and root soil of different Acacia species. The most dominant phylum in the rhizosphere soil was Acidobacteria, followed by Proteobacteria and Actinobacteria, whereas the dominant phylum in the root soil was Proteobacteria, followed by Actinobacteria and Acidobacteria. Among the various Acacia species, specific bacterial communities displayed different abundance. We systematically described the core bacteria in the rhizosphere and root endophytic bacterial communities and predicted their relevant functions. The type and abundance of specific bacteria were correlated with the nutrient absorption and metabolism of the Acacia species. This study addresses the complex host-microbe interactions and explores the rhizosphere and root bacterial community structure of different Acacia species. These results provide new insights into the role of rhizosphere and root endophytic bacterial communities on the growth and reproduction of Acacia, thus informing future efforts towards sustainable development and utilization of Acacia.

APA, Harvard, Vancouver, ISO, and other styles

24

Sritongon, Natthawat, Sophon Boonlue, Wiyada Mongkolthanaruk, Sanun Jogloy, and Nuntavun Riddech. "Impact of Rhizobacterial Inoculants and Organic Amendment on Bacterial Communities of Jerusalem artichoke Tissue and Rhizosphere by using Denaturing Gradient Gel Electrophoresis." Chiang Mai Journal of Science 50, no. 5 (September 29, 2023): 1–16. http://dx.doi.org/10.12982/cmjs.2023.051.

Full text

Abstract:

The application of organic amendments can improve soil quality and influence bacterial communities, contributing to enhanced soil health in agricultural systems. This study investigated the effect of using rain tree leaf, corn husk, and peat moss as soil amendments, supplemented with plant growth promoting rhizobacteria on communities of bacteria in the tissue and rhizosphere of Jerusalem artichoke. The plants were observed for 120 days after transplanting. Polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) technique was used to investigate the impact of both organic amendments and bacterial consortium with comparative profiles. Comparison DGGE profile by clustering analysis did not clearly separate each organic amendment and bacterial inoculation, but principal component analysis (PCA) revealed that plant age had an influence on tissue and rhizosphere bacterial communities. The results indicated that soil amendments and bacterial inoculation had no effect on bacterial community shifts. Interestingly, the genera of bacteria able to most colonize in the tissue and rhizosphere were the uncultured bacteria. Thus, we provide promising data for boosting Jerusalem artichoke growth and soil quality with potential organic amendments to improve soil with sustainable strategies.

APA, Harvard, Vancouver, ISO, and other styles

25

Liu, Shaodong, Ruihua Liu, Siping Zhang, Qian Shen, Jing Chen, Huijuan Ma, Changwei Ge, et al. "The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil–Root Continuum Niche Gradient." Microorganisms 12, no. 5 (April 26, 2024): 869. http://dx.doi.org/10.3390/microorganisms12050869.

Full text

Abstract:

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum.

APA, Harvard, Vancouver, ISO, and other styles

26

Shi, Yikai, Xuruo Wang, Huifeng Cai, Jiangdong Ke, Jinyong Zhu, Kaihong Lu, Zhongming Zheng, and Wen Yang. "The Assembly Process of Free-Living and Particle-Attached Bacterial Communities in Shrimp-Rearing Waters: The Overwhelming Influence of Nutrient Factors Relative to Microalgal Inoculation." Animals 13, no. 22 (November 11, 2023): 3484. http://dx.doi.org/10.3390/ani13223484.

Full text

Abstract:

The ecological functions of bacterial communities vary between particle-attached (PA) lifestyles and free-living (FL) lifestyles, and separately exploring their community assembly helps to elucidate the microecological mechanisms of shrimp rearing. Microalgal inoculation and nutrient enrichment during shrimp rearing are two important driving factors that affect rearing-water bacterial communities, but their relative contributions to the bacterial community assembly have not been evaluated. Here, we inoculated two microalgae, Nannochloropsis oculata and Thalassiosira weissflogii, into shrimp-rearing waters to investigate the distinct effects of various environmental factors on PA and FL bacterial communities. Our study showed that the composition and representative bacteria of different microalgal treatments were significantly different between the PA and FL bacterial communities. Regression analyses and Mantel tests revealed that nutrients were vital factors that constrained the diversity, structure, and co-occurrence patterns of both the PA and FL bacterial communities. Partial least squares path modeling (PLS-PM) analysis indicated that microalgae could directly or indirectly affect the PA bacterial community through nutrient interactions. Moreover, a significant interaction was detected between PA and FL bacterial communities. Our study reveals the unequal effects of microalgae and nutrients on bacterial community assembly and helps explore microbial community assembly in shrimp-rearing ecosystems.

APA, Harvard, Vancouver, ISO, and other styles

27

Mohamed, Naglaa M., Julie J. Enticknap, Jayme E. Lohr, Scott M. McIntosh, and Russell T. Hill. "Changes in Bacterial Communities of the Marine Sponge Mycale laxissima on Transfer into Aquaculture†." Applied and Environmental Microbiology 74, no. 4 (December 21, 2007): 1209–22. http://dx.doi.org/10.1128/aem.02047-07.

Full text

Abstract:

ABSTRACT The changes in bacterial communities associated with the marine sponge Mycale laxissima on transfer to aquaculture were studied using culture-based and molecular techniques. M. laxissima was maintained alive in flowthrough and closed recirculating aquaculture systems for 2 years and 1 year, respectively. The bacterial communities associated with wild and aquacultured sponges, as well as the surrounding water, were assessed using 16S rRNA gene clone library analysis and denaturing gradient gel electrophoresis (DGGE). Bacterial richness and diversity were measured using DOTUR computer software, and clone libraries were compared using S-LIBSHUFF. DGGE analysis revealed that the diversity of the bacterial community of M. laxissima increased when sponges were maintained in aquaculture and that bacterial communities associated with wild and aquacultured M. laxissima were markedly different than those of the corresponding surrounding water. Clone libraries of bacterial 16S rRNA from sponges confirmed that the bacterial communities changed during aquaculture. These communities were significantly different than those of seawater and aquarium water. The diversity of bacterial communities associated with M. laxissima increased significantly in aquaculture. Our work shows that it is important to monitor changes in bacterial communities when examining the feasibility of growing sponges in aquaculture systems because these communities may change. This could have implications for the health of sponges or for the production of bioactive compounds by sponges in cases where these compounds are produced by symbiotic bacteria rather than by the sponges themselves.

APA, Harvard, Vancouver, ISO, and other styles

28

Telang, Anita J., Gerrit Voordouw, Sara Ebert, Neili Sifeldeen, Julia M. Foght, Phillip M. Fedorak, and D. W. S. Westlake. "Characterization of the diversity of sulfate-reducing bacteria in soil and mining waste water environments by nucleic acid hybridization techniques." Canadian Journal of Microbiology 40, no. 11 (November 1, 1994): 955–64. http://dx.doi.org/10.1139/m94-152.

Full text

Abstract:

Nucleic acid hybridization techniques were used to characterize the sulfate-reducing bacterial communities at seven waste water and two soil sites in Canada. Genomic DNA was obtained from liquid enrichment cultures of samples taken from these nine sites. The liquid enrichment protocol favored growth of the sulfate-reducing bacterial component of the communities at these sites. The genomic DNA preparations were analyzed with (i) a specific gene probe aimed at a single genus (Desulfovibrio), (ii) a general 16S rRNA gene probe aimed at all genera of sulfate-reducing bacteria and other bacteria, and (iii) whole genome probes aimed at specific bacteria. This three-pronged approach provided information on the sulfate-reducing bacterial community structures for the nine sites. These were compared with each other and with the sulfate-reducing bacterial communities of western Canadian oil field production waters, studied previously. It was found that there is considerable diversity in the sulfate-reducing bacterial community at each site. Most sulfate-reducing bacteria isolated from distinct sites are genomically different and differ also from sulfate-reducing bacteria found in oil field production waters.Key words: sulfate-reducing bacteria, genomic diversity, nucleic acid hybridization, microbial community.

APA, Harvard, Vancouver, ISO, and other styles

29

Wang, Cheng-yu, Xue Zhou, Dan Guo, Jiang-hua Zhao, Li Yan, Guo-zhong Feng, Qiang Gao, Han Yu, and Lan-po Zhao. "Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China." Annals of Microbiology 69, no. 13 (December 2019): 1461–73. http://dx.doi.org/10.1007/s13213-019-01529-9.

Full text

Abstract:

Abstract Purpose To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil. Method A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions. Result The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

APA, Harvard, Vancouver, ISO, and other styles

30

Lin, Chorng-Horng, Chih-Hsiang Chuang, Wen-Hung Twan, Shu-Fen Chiou, Tit-Yee Wong, Jong-Kang Liu, Chyuan-yao Kao, and Jimmy Kuo. "Seasonal changes in bacterial communities associated with healthy and diseasedPoritescoral in southern Taiwan." Canadian Journal of Microbiology 62, no. 12 (December 2016): 1021–33. http://dx.doi.org/10.1139/cjm-2016-0100.

Full text

Abstract:

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

APA, Harvard, Vancouver, ISO, and other styles

31

Jia, Meiqing, Zhiwei Gao, Huijun Gu, Chenyu Zhao, Meiqi Liu, Fanhui Liu, Lina Xie, et al. "Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe." PLOS ONE 16, no. 3 (March 17, 2021): e0248194. http://dx.doi.org/10.1371/journal.pone.0248194.

Full text

Abstract:

Currently, the impact of changes in precipitation and increased nitrogen(N) deposition on ecosystems has become a global problem. In this study, we conducted a 8-year field experiment to evaluate the effects of interaction between N deposition and precipitation change on soil bacterial communities in a desert steppe using high-throughput sequencing technology. The results revealed that soil bacterial communities were sensitive to precipitation addition but were highly tolerant to precipitation reduction. Reduced precipitation enhanced the competitive interactions of soil bacteria and made the ecological network more stable. Nitrogen addition weakened the effect of water addition in terms of soil bacterial diversity and community stability, and did not have an interactive influence. Moreover, decreased precipitation and increased N deposition did not have a superimposed effect on soil bacterial communities in the desert steppe. Soil pH, moisture content, and NH4+-N and total carbon were significantly related to the structure of bacterial communities in the desert steppe. Based on network analysis and relative abundance, we identified Actinobacteria, Proteobacteria, Acidobacteria and Cyanobacteria members as the most important keystone bacteria that responded to precipitation changes and N deposition in the soil of the desert steppe. In summary, we comprehensively analyzed the responses of the soil bacterial community to precipitation changes and N deposition in a desert steppe, which provides a model for studying the effects of ecological factors on bacterial communities worldwide.

APA, Harvard, Vancouver, ISO, and other styles

32

Zhang, Mingyue, Yanan Zhou, Xinyuan Cui, and Lifeng Zhu. "The Potential of Co-Evolution and Interactions of Gut Bacteria–Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis." Microorganisms 12, no. 4 (March 31, 2024): 713. http://dx.doi.org/10.3390/microorganisms12040713.

Full text

Abstract:

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host’s physiological development and immune health. A phage is a virus that directly infects bacteria, and phages’ close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial–phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

APA, Harvard, Vancouver, ISO, and other styles

33

Weitzman, Chava L., Lisa K. Belden, Meghan May, Marissa M. Langager, Rami A. Dalloul, and Dana M. Hawley. "Antibiotic perturbation of gut bacteria does not significantly alter host responses to ocular disease in a songbird species." PeerJ 10 (June 10, 2022): e13559. http://dx.doi.org/10.7717/peerj.13559.

Full text

Abstract:

Bacterial communities in and on wild hosts are increasingly appreciated for their importance in host health. Through both direct and indirect interactions, bacteria lining vertebrate gut mucosa provide hosts protection against infectious pathogens, sometimes even in distal body regions through immune regulation. In house finches (Haemorhous mexicanus), the bacterial pathogen Mycoplasma gallisepticum (MG) causes conjunctivitis, with ocular inflammation mediated by pro- and anti-inflammatory cytokines and infection triggering MG-specific antibodies. Here, we tested the role of gut bacteria in host responses to MG by using oral antibiotics to perturb bacteria in the gut of captive house finches prior to experimental inoculation with MG. We found no clear support for an impact of gut bacterial disruption on conjunctival pathology, MG load, or plasma antibody levels. However, there was a non-significant trend for birds with intact gut communities to have greater conjunctival pathology, suggesting a possible impact of gut bacteria on pro-inflammatory cytokine stimulation. Using 16S bacterial rRNA amplicon sequencing, we found dramatic differences in cloacal bacterial community composition between captive, wild-caught house finches in our experiment and free-living finches from the same population, with lower bacterial richness and core communities composed of fewer genera in captive finches. We hypothesize that captivity may have affected the strength of results in this experiment, necessitating further study with this consideration. The abundance of anthropogenic impacts on wildlife and their bacterial communities, alongside the emergence and spread of infectious diseases, highlights the importance of studies addressing the role of commensal bacteria in health and disease, and the consequences of gut bacterial shifts on wild hosts.

APA, Harvard, Vancouver, ISO, and other styles

34

Hartman, Wyatt H., Curtis J. Richardson, Rytas Vilgalys, and Gregory L. Bruland. "Environmental and anthropogenic controls over bacterial communities in wetland soils." Proceedings of the National Academy of Sciences 105, no. 46 (November 12, 2008): 17842–47. http://dx.doi.org/10.1073/pnas.0808254105.

Full text

Abstract:

Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status.

APA, Harvard, Vancouver, ISO, and other styles

35

Pires, A. C. C., D. F. R. Cleary, A. R. M. Polónia, S. C. Lim, N. J. De Voogd, V. Oliveira, and N. C. M. Gomes. "Comparison of bacterial communities associated withXestospongia testudinaria, sediment and seawater in a Singaporean coral reef ecosystem." Journal of the Marine Biological Association of the United Kingdom 99, no. 2 (April 2, 2018): 331–42. http://dx.doi.org/10.1017/s0025315418000188.

Full text

Abstract:

Despite alterations caused by anthropogenic activities in Singaporean coral reefs, the sponge communities are quite diverse andXestospongia testudinariais one of the most common sponge species. In the present study, we used 16S rRNA gene barcoded pyrosequencing to characterize and compare bacterial communities from different biotopes (sponge, seawater and sediment) and to identify dominant bacterial symbionts ofX. testudinariain a Singaporean coral reef ecosystem. Our results showed that biotope appears to affect the richness, composition and abundance of bacterial communities. Proteobacteria was the most abundant phylum in sediment and seawater whilst Chloroflexi was more abundant inX. testudinaria.Members of the order Caldilineales (fermentation of organic substrates), Chromatiales (purple sulphur bacteria), Rhodospirillales (purple non-sulphur bacteria) and Syntrophobacterales (sulphate-reducing bacteria) were relatively more abundant inX. testudinariasamples.

APA, Harvard, Vancouver, ISO, and other styles

36

Liang, Tianyu, Guang Yang, Yunxia Ma, Qingzhi Yao, Yuan Ma, Hui Ma, Yang Hu, et al. "Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China." PeerJ 7 (August 22, 2019): e7526. http://dx.doi.org/10.7717/peerj.7526.

Full text

Abstract:

The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.

APA, Harvard, Vancouver, ISO, and other styles

37

Xie, Wan-Ying, Jian-Qiang Su, and Yong-Guan Zhu. "Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing." Applied and Environmental Microbiology 81, no. 2 (October 31, 2014): 522–32. http://dx.doi.org/10.1128/aem.03191-14.

Full text

Abstract:

ABSTRACTThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We tookWolffia australianaas a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere ofW. australianaharbored considerably rich communities of bacteria, withProteobacteriaandBacteroidetesas the predominant phyla. The core microbiome in the phyllosphere contained genera such asAcidovorax,Asticcacaulis,Methylibium, andMethylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.

APA, Harvard, Vancouver, ISO, and other styles

38

Ma, Kang, Ze Ren, Jiaming Ma, Nannan Chen, and Jingling Liu. "Compositional Changes and Co-Occurrence Patterns of Planktonic Bacteria and Microeukaryotes in a Subtropical Estuarine Ecosystem, the Pearl River Delta." Water 14, no. 8 (April 11, 2022): 1227. http://dx.doi.org/10.3390/w14081227.

Full text

Abstract:

Planktonic microorganisms in aquatic ecosystems form complex assemblages of highly interactive taxa and play key roles in biogeochemical cycles. However, the microbial interactions within bacterial and microeukaryotic communities, and the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances in the river estuary remain unknown. Here, 16S and 18S rRNA gene sequencing were used to investigate the compositional changes and the co-occurrence patterns of bacterial and microeukaryotic communities. The results showed that the rare taxa in the bacterial communities were more prevalent than those in the microeukaryotic communities and may influence the resilience and resistance of microorganisms to environmental variations in estuarine ecosystems. The environmental variations had strong effects on the microeukaryotic communities and their assembly mechanisms but not on the bacterial communities in our studied area. However, based on co-occurrence network analyses, the bacterial communities had stronger links and more complex interactions than microeukaryotic communities, suggesting that bacterial networks may help improve the buffering capacities of the estuarine ecosystem against environmental change. The keystone taxa of bacteria mainly belonged to rare subcommunities, which further illustrates that rare taxa may play fundamental roles in network persistence. Overall, these results provide insights into the microbial responses of aquatic ecosystems to environmental heterogeneity.

APA, Harvard, Vancouver, ISO, and other styles

39

Dangerfield, Cody R., Nalini M. Nadkarni, and William J. Brazelton. "Canopy soil bacterial communities altered by severing host tree limbs." PeerJ 5 (September 6, 2017): e3773. http://dx.doi.org/10.7717/peerj.3773.

Full text

Abstract:

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

APA, Harvard, Vancouver, ISO, and other styles

40

Kudinova, Alina G., Andrey V. Dolgih, Nikita S. Mergelov, Ilya G. Shorkunov, Olga A. Maslova, and Mayya A. Petrova. "The Abundance and Taxonomic Diversity of Filterable Forms of Bacteria during Succession in the Soils of Antarctica (Bunger Hills)." Microorganisms 9, no. 8 (August 13, 2021): 1728. http://dx.doi.org/10.3390/microorganisms9081728.

Full text

Abstract:

Previous studies have shown that a significant part of the bacterial communities of Antarctic soils is represented by cells passing through filters with pore sizes of 0.2 µm. These results raised new research questions about the composition and diversity of the filterable forms of bacteria (FFB) in Antarctic soils and their role in the adaptation of bacteria to the extreme living conditions. To answer such questions, we analyzed the succession of bacterial communities during incubation of Antarctic soil samples from the Bunger Hills at increased humidity and positive temperatures (5 °C and 20 °C). We determined the total number of viable cells by fluorescence microscopy in all samples and assessed the taxonomic diversity of bacteria by next-generation sequencing of the 16S rRNA gene region. Our results have shown that at those checkpoints where the total number of cells reached the maximum, the FFB fraction reached its minimum, and vice versa. We did not observe significant changes in taxonomic diversity in the soil bacterial communities during succession. During our study, we found that the soil bacterial communities as a whole and the FFB fraction consist of almost the same phylogenetic groups. We suppose rapid transition of the cells of the active part of the bacterial population to small dormant forms is one of the survival strategies in extreme conditions and contributes to the stable functioning of microbial communities in Antarctic soils.

APA, Harvard, Vancouver, ISO, and other styles

41

Acosta, Kenneth, Shawn Sorrels, William Chrisler, Weijuan Huang, Sarah Gilbert, Thomas Brinkman, Todd P. Michael, Sarah L. Lebeis, and Eric Lam. "Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria." Plants 12, no. 4 (February 15, 2023): 872. http://dx.doi.org/10.3390/plants12040872.

Full text

Abstract:

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

APA, Harvard, Vancouver, ISO, and other styles

42

Woodcock, Stephen, Christopher J. Van Der Gast, Thomas Bell, Mary Lunn, Thomas P. Curtis, Ian M. Head, and William T. Sloan. "Neutral assembly of bacterial communities." FEMS Microbiology Ecology 62, no. 2 (November 2007): 171–80. http://dx.doi.org/10.1111/j.1574-6941.2007.00379.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

43

Römling, Ute. "Bacterial communities as capitalist economies." Nature 497, no. 7449 (May 2013): 321–22. http://dx.doi.org/10.1038/nature12103.

Full text

APA, Harvard, Vancouver, ISO, and other styles

44

Park, Chae Haeng, Kyung Mo Kim, Ok-Sun Kim, Gajin Jeong, and Soon Gyu Hong. "Bacterial communities in Antarctic lichens." Antarctic Science 28, no. 6 (August 3, 2016): 455–61. http://dx.doi.org/10.1017/s0954102016000286.

Full text

Abstract:

AbstractTo date, many studies surveying the bacterial communities in lichen thalli from diverse geographical areas have shown that Alphaproteobacteria is the predominant bacterial class in most lichens. In this study, bacterial communities in several Antarctic lichens with different growth form and substrates were analysed. The bacterial community composition in fruticose and foliose lichens, Cladonia, Umbilicaria and Usnea, and crustose lichens, Buelia granulosa, Amandinea coniops and Ochrolechia parella, from King George Island was analysed by pyrosequencing of bacterial 16S rRNA genes. Results showed that Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were predominant phyla. The predominant bacterial class in most of the samples was Alphaproteobacteria. Acetobacteriaceae of the order Rhodospiralles in Alphaproteobacteria was the most abundant bacterial family in Antarctic lichens. The LAR1 lineage of the order Rhizobiales, a putative N-fixer which has been frequently observed in lichens from temperate areas, was detected only from a few samples at low frequency. It is expected that other bacterial taxa are working as N-fixers in Antarctic lichens. From the PCoA analysis of the Fast UniFrac distance matrix, it was proposed that the microbial community structures in Antarctic lichens were affected by host species, growth form and substrates.

APA, Harvard, Vancouver, ISO, and other styles

45

Fridman, Svetlana, Ido Izhaki, Yoram Gerchman, and Malka Halpern. "Bacterial communities in floral nectar." Environmental Microbiology Reports 4, no. 1 (November 29, 2011): 97–104. http://dx.doi.org/10.1111/j.1758-2229.2011.00309.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

Denk-Lobnig, Marlis, and Kevin B. Wood. "Antibiotic resistance in bacterial communities." Current Opinion in Microbiology 74 (August 2023): 102306. http://dx.doi.org/10.1016/j.mib.2023.102306.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Gottesman, Susan. "Traveling with Terri: bacterial communities." Genes & Development 37, no. 1-2 (January 1, 2023): 27–29. http://dx.doi.org/10.1101/gad.350469.123.

Full text

APA, Harvard, Vancouver, ISO, and other styles

48

Zhang, Xiaohan, Ying Zhang, Nan Wu, Wenjie Li, Xiaocui Song, Yongzheng Ma, and Zhiguang Niu. "Colonization characteristics of bacterial communities on plastic debris: The localization of immigrant bacterial communities." Water Research 193 (April 2021): 116883. http://dx.doi.org/10.1016/j.watres.2021.116883.

Full text

APA, Harvard, Vancouver, ISO, and other styles

49

Azzoni, Roberto Sergio, Ilario Tagliaferri, Andrea Franzetti, Christoph Mayer, Astrid Lambrecht, Chiara Compostella, Marco Caccianiga, et al. "Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya." Annals of Glaciology 59, no. 77 (September 12, 2018): 10–20. http://dx.doi.org/10.1017/aog.2018.18.

Full text

Abstract:

ABSTRACTSnow can be considered an independent ecosystem that hosts active microbial communities. Snow microbial communities have been extensively investigated in the Arctic and in the Antarctica, but rarely in mid-latitude mountain areas. In this study, we investigated the bacterial communities of snow collected in four glacierized areas (Alps, Eastern Anatolia, Karakoram and Himalaya) by high-throughput DNA sequencing. We also investigated the origin of the air masses that produced the sampled snowfalls by reconstructing back-trajectories. A standardized approach was applied to all the analyses in order to ease comparison among different communities and geographical areas. The bacterial communities hosted from 25 to 211 Operational Taxonomic Units (OTUs), and their structure differed significantly between geographical areas. This suggests that snow bacterial communities may largely derive from ‘local’ air bacteria, maybe by deposition of airborne particulate of local origin that occurs during snowfall. However, some evidences suggest that a contribution of bacteria collected during air mass uplift to snow communities cannot be excluded, particularly when the air mass that originated the snow event is particularly rich in dust.

APA, Harvard, Vancouver, ISO, and other styles

50

Cheng, Dandan, Zhongsai Tian, Liang Feng, Lin Xu, and Hongmei Wang. "Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range." PeerJ 6 (January 7, 2019): e6162. http://dx.doi.org/10.7717/peerj.6162.

Full text

Abstract:

Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Bacterial communities'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles