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Journal articles on the topic 'Bacterial diversity'

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Published: 4 June 2021
Last updated: 20 February 2023

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1

Han, J., L. Y. Wang, and B. Y. Cai. "Bacterial diversity in antibiotic wastewater treatment." Water Science and Technology 68, no. 12 (October 24, 2013): 2676–82. http://dx.doi.org/10.2166/wst.2013.529.

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The bacterial diversity of an antibiotic industrial wastewater treatment system was analyzed to provide the information required for further optimization of this process and for identification of bacterial strains that perform improved degradation of antibiotic industrial wastewater. The total bacterial DNA of samples collected at three stages (aeration, precipitation, and idle) during the sequencing batch reactor (SBR) process were analyzed by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) of the 16 s rDNA V3 regions. Community analysis was conducted in terms of the richness value (S), the dominance degree and the Shannon–Wiener diversity index (H). Rich bacterial diversity was apparent in the aeration stage of the SBR process, and the number of bands in the aeration stage was more abundant than that in the precipitation and idle stages. The DGGE analysis showed 15 bands, six of which were uncultured bacteria, and included one anaerobic and five aerobic bacteria. The microbial community in the aeration stage was the most complex of the whole SBR process, while the dominant bacteria differed in each reaction stage. These results demonstrate the cyclical dynamic changes in the bacterial population during the SBR process for the treatment of antibiotic industrial wastewater.
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2

López-Lara, Isabel M., and Otto Geiger. "Bacterial lipid diversity." Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1862, no. 11 (November 2017): 1287–99. http://dx.doi.org/10.1016/j.bbalip.2016.10.007.

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3

He, Yuanhao, Xiaojun Deng, and Feng Che. "Genetic diversity and community structure of soil bacteria in Chinese fir plantations." Soil and Water Research 14, No. 1 (January 23, 2019): 22–31. http://dx.doi.org/10.17221/10/2018-swr.

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To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.
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4

Chiba, Akane, Yoshitaka Uchida, Susanne Kublik, Gisle Vestergaard, Franz Buegger, Michael Schloter, and Stefanie Schulz. "Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition." Microorganisms 9, no. 2 (February 11, 2021): 357. http://dx.doi.org/10.3390/microorganisms9020357.

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This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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5

Mushegian, Alexandra A., Celeste N. Peterson, Christopher C. M. Baker, and Anne Pringle. "Bacterial Diversity across Individual Lichens." Applied and Environmental Microbiology 77, no. 12 (April 29, 2011): 4249–52. http://dx.doi.org/10.1128/aem.02850-10.

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ABSTRACTSymbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities.
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6

Godon, Jean-Jacques, Emmanuelle Zumstein, Patrick Dabert, Frédéric Habouzit, and René Moletta. "Microbial 16S rDNA diversity in an anaerobic digester." Water Science and Technology 36, no. 6-7 (September 1, 1997): 49–55. http://dx.doi.org/10.2166/wst.1997.0574.

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The bacterial community structure of a fluidized bed reactor fed by vinasses was analysed by molecular identification. After PCR amplification, three 16S rDNA clone libraries of Bacteria, Archaea, and Procarya populations were established. Community structure was determined by phylogenetic analysis of 556 partial rDNA sequences (about 500 bp long). 139 OTUs (Operational Taxonomic Unit) were found among which 133 and 6 were from the Bacteria and Archaea domains respectively. The majority of bacterial OTUs are not closely related to all other hitherto-determined sequences. The ratio Archaea/Bacteria is 1/4 and the most frequent bacterial OTU represents less than 5% of the characterised bacterial population.
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7

Chin, Lai Mun, and Vui Ling Clemente Michael Wong. "Tropical Soil Bacterial Diversity in Sabah, Malaysia." Sains Malaysiana 51, no. 2 (February 28, 2022): 451–60. http://dx.doi.org/10.17576/jsm-2022-5102-10.

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Bacteria are an essential biological component of soil function that plays fundamental roles in biogeochemical cycling, soil quality improvement, habitat-shaping, and ecosystem conservation. It is therefore important to have a good record of soil bacteria in the tropics in order to monitor future changes that may occur due to global warming and other factors. However, extremely limited data are available on the diversity of bacteria in soils in some tropical Borneo regions such as Sabah, Malaysia. This research, therefore, was undertaken to determine the bacterial diversity of soils from various locations in Sabah, Malaysia. Ten soil samples (n=10) were collected around Sabah. 16S rDNA of bacterial DNA extracted from soils were amplified and analysed using the Denaturing Gradient Gel Electrophoresis (DGGE). A total of 100 dominant and well-defined DNA fragments observed in the DGGE gel were extracted, sequenced, and aligned. The results indicated that 93 different bacterial operational taxonomic units (OTUs) representing bacteria from 8 different phyla were present. The most abundant phyla in the analysed Sabah soils were Proteobacteria followed by Acidobacteria, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia, Chloroflexi, and Bacteroidetes. The examined soils of Sabah and Peninsular Malaysia had similar dominant phyla in general, except that the most dominant phylum in Peninsular Malaysia soils is the Acidobacteria instead of Proteobacteria. These baseline data generated from this work are important and can be used to track bacterial diversity shifts due to soil or environmental changes in the future.
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8

Haynes, S., A. C. Darby, T. J. Daniell, G. Webster, F. J. F. van Veen, H. C. J. Godfray, J. I. Prosser, and A. E. Douglas. "Diversity of Bacteria Associated with Natural Aphid Populations." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7216–23. http://dx.doi.org/10.1128/aem.69.12.7216-7223.2003.

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ABSTRACT The bacterial communities of aphids were investigated by terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments generated by PCR with general eubacterial primers. By both methods, theγ -proteobacterium Buchnera was detected in laboratory cultures of six parthenogenetic lines of the pea aphid Acyrthosiphon pisum and one line of the black bean aphid Aphis fabae, and one or more of four previously described bacterial taxa were also detected in all aphid lines except one of A. pisum. These latter bacteria, collectively known as secondary symbionts or accessory bacteria, comprised three taxa of γ-proteobacteria (R-type [PASS], T-type [PABS], and U-type [PAUS]) and a rickettsia (S-type [PAR]). Complementary analysis of aphids from natural populations of four aphid species (A. pisum [n= 74], Amphorophora rubi [n= 109], Aphis sarothamni [n= 42], and Microlophium carnosum [n= 101]) from a single geographical location revealed Buchnera and up to three taxa of accessory bacteria, but no other bacterial taxa, in each aphid. The prevalence of accessory bacterial taxa varied significantly among aphid species but not with the sampling month (between June and August 2000). These results indicate that the accessory bacterial taxa are distributed across multiple aphid species, although with variable prevalence, and that laboratory culture does not generally result in a shift in the bacterial community in aphids. Both the transmission patterns of the accessory bacteria between individual aphids and their impact on aphid fitness are suggested to influence the prevalence of accessory bacterial taxa in natural aphid populations.
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9

Kennedy, A. C. "Bacterial diversity in agroecosystems." Agriculture, Ecosystems & Environment 74, no. 1-3 (June 1999): 65–76. http://dx.doi.org/10.1016/s0167-8809(99)00030-4.

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10

Beckwith, Jon. "Genetics of bacterial diversity." Trends in Genetics 5 (1989): 348. http://dx.doi.org/10.1016/0168-9525(89)90141-8.

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11

Danchin, A. "Genetics of bacterial diversity." Biochimie 74, no. 6 (June 1992): 594. http://dx.doi.org/10.1016/0300-9084(92)90173-c.

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12

Reuben, S., C. L. N. Chua, K. D. Fam, Z. Y. A. Thian, M. K. Kang, and S. Swarup. "Bacterial diversity on different surfaces in urban freshwater." Water Science and Technology 65, no. 10 (May 1, 2012): 1869–74. http://dx.doi.org/10.2166/wst.2012.952.

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Microbial loads in freshwater systems have important implications in biogeochemical cycling in urban environments. Immersed surfaces in freshwaters provide surfaces for bacterial attachment and growth. Microorganisms that adhere initially to these surfaces play a critical role in biofilm formation and sustenance. Currently, there is little understanding on the type of organisms that initially adhere to different surfaces in urban canals. In this study, water from an urban stormwater canal was employed to allow bacteria to attach to different surfaces in a flowcell apparatus and understand the differences and changes in bacterial community structure. Bacterial communities were highly diverse on different surfaces as indicated by Jaccard's indices of 0.14–0.56. Bacteria on aluminium were the most diverse and on Plexiglas the least. Bacterial communities were highly dynamic in the early attachment phase and it changed by 59% between 3 and 6 h on aluminium. Specificity of attachment to surfaces was observed for some bacteria. Judicious use of materials in urban aquatic environment would help mitigate microbial load in urban waters.
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13

KOSOY, M., C. MCKEE, L. ALBAYRAK, and Y. FOFANOV. "Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives." Parasitology 145, no. 5 (August 2, 2017): 543–62. http://dx.doi.org/10.1017/s0031182017001263.

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SUMMARYGrowing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.
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14

Zeng, Quanchao, and Shaoshan An. "Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau." Microorganisms 9, no. 1 (January 9, 2021): 139. http://dx.doi.org/10.3390/microorganisms9010139.

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High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.
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15

Zeng, Quanchao, and Shaoshan An. "Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau." Microorganisms 9, no. 1 (January 9, 2021): 139. http://dx.doi.org/10.3390/microorganisms9010139.

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High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.
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16

Balint-Kurti, Peter, Susan J. Simmons, James E. Blum, Carlos L. Ballaré, and Ann E. Stapleton. "Maize Leaf Epiphytic Bacteria Diversity Patterns Are Genetically Correlated with Resistance to Fungal Pathogen Infection." Molecular Plant-Microbe Interactions® 23, no. 4 (April 2010): 473–84. http://dx.doi.org/10.1094/mpmi-23-4-0473.

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Plant leaves host a specific set of microbial epiphytes. Plant genetic and solar UV-B radiation effects on the diversity of the phyllosphere were examined by measuring epiphytic bacterial ribosomal DNA diversity in a maize recombinant inbred (RI) mapping population. Several chromosomal quantitative trait loci (QTL) with significant effects on bacterial diversity were identified, some of which had effects only in the presence of UV-B radiation and others that had effects both with and without UV-B. Candidate genes with allele-specific effects were mapped to the bacterial diversity chromosomal regions. A glutamate decarboxylase candidate gene was located at a UV-B–specific chromosomal locus, and in a comparison between two RI lines with contrasting bacterial diversity phenotypes, high bacterial diversity was associated with high levels of glutamate decarboxylase enzyme activity, a component of the gamma-aminobutyric acid (GABA) pathway. The bacterial diversity loci exhibited a significant overlap with loci connected with Southern leaf blight (SLB) susceptibility in the field. A SLB-resistant inbred genotype had less beta bacterial diversity, and antibiotic treatment of inbreds increased this diversity. These results suggest that the GABA pathway is genetically associated with phyllosphere bacterial diversity. Furthermore, the colocalization of QTL between low bacterial diversity and fungal blight–resistance and the increase in beta diversity in antibiotic-treated leaves suggest that occupation of leaf habitats by a particular set of suppressive bacteria may restrict phyllosphere bacterial variability and increase resistance to fungal infection.
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17

Yan, Yao, Bingjun Li, Zhijun Huang, Hui Zhang, Xiaojian Wu, Taimoor Hassan Farooq, Pengfei Wu, Ming Li, and Xiangqing Ma. "Characteristics and Driving Factors of Rhizosphere Bacterial Communities of Chinese Fir Provenances." Forests 12, no. 10 (October 8, 2021): 1362. http://dx.doi.org/10.3390/f12101362.

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Rhizosphere bacteria affect the diversity of soil functions, playing important roles in the growth and expansion of Chinese fir. Understanding the driving factors of rhizosphere bacterial distribution is imperative when comparing bacterial diversity and composition under different Chinese fir provenances. We investigated the growth of Chinese fir belts and the effects of climate, geographic location, and soil nutrients. Using 16S rDNA next-generation sequencing analysis, the bacterial communities of 16 Chinese fir provenances were compared. The bacterial compositionsof Dechang, Junlian, Shangrao, Zhenxiong, Yangxin, Xinyang, Luotian, and Tianmushan provenances weredistinct from others. Generally, higher-latitude provenances showed more biomarkers (LDA = 2). Rhizosphere bacterial α-diversity was the highest in Hunan Youxian and lowest in Henan Xinyang (p < 0.05). From south to north, bacterial α-diversity initially increased and then decreased. From east to west in the middle belt, bacterial α-diversity followed a “W” trend, with the eastern middle belt having the highest values, especially near Hunan, Fujian, and Zhejiang provinces. Amongst environmental factors, soil nutrient content (Mg, P and K) and stoichiometric ratio (Ca/Mg, K/Ca and N/P), along with precipitationrate primarily controlled rhizosphere bacterial diversity. Soil pH had a significant impact on the relative abundance of rhizosphere soil bacteria. Our findings offer insight into the evolution of Chinese fir and provide a scientific basis for soil microbial community improvement of Chinese fir provenances.
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18

Zhang, Hongying, Zongjun Gao, Mengjie Shi, and Shaoyan Fang. "Soil Bacterial Diversity and Its Relationship with Soil CO2 and Mineral Composition: A Case Study of the Laiwu Experimental Site." International Journal of Environmental Research and Public Health 17, no. 16 (August 7, 2020): 5699. http://dx.doi.org/10.3390/ijerph17165699.

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To better understand the characteristics of soil bacterial diversity in different environments, the Laiwu Qilongwan experimental site was selected as it is of great significance for the study of geochemical cycles. The soil CO2, mineral composition and bacterial community were analyzed by an EGM-4 portable environmental gas detector, an X-ray diffractometer and 16S rDNA high-throughput sequencing, and soil bacterial diversity and the relationship between soil bacterial diversity and environmental factors were studied. The results showed that with increasing soil depth, the CO2 content increased, the feldspar and amphibole contents increased, the quartz content decreased, the richness of the soil bacterial community increased, the relative richness of Nitrospirae increased, and Chloroflexi decreased. The dominant bacteria were Proteobacteria, Actinobacteria and Acidobacteria. There were slight differences in soil CO2, mineral composition and dominant bacterial flora at the same depth. Actinobacteria, Proteobacteria and Firmicutes were the dominant phyla of L02. The CO2 was lowest in bare land, and the quartz and K-feldspar contents were the highest. Soil CO2 mainly affected the deep bacterial diversity, while shallow soil bacteria were mainly affected by mineral components (quartz and K-feldspar). At the same depth, amphibole and clay minerals had obvious effects on the bacterial community, while CO2 had obvious effects on subdominant bacteria.
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19

Kuang, Shaoping, Yaqing Su, Huihui Wang, Wenjuan Yu, Qiaolin Lang, and Ravichandra Matangi. "Soil Microbial Community Structure and Diversity around the Aging Oil Sludge in Yellow River Delta as Determined by High-Throughput Sequencing." Archaea 2018 (August 30, 2018): 1–10. http://dx.doi.org/10.1155/2018/7861805.

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Microorganisms are sensitive indicators of edaphic environmental variation. The Illumina MiSeq sequencing technology was used to analyze soil bacterial community diversity around an aging oil sludge in the Yellow River Delta. The alpha diversity index of soil bacterial community results (Ace, Chao, Shannon, and Simpson) determined that bacterial community diversity sampling within the scope of a 20 cm radius from the center of an aging oil sludge spot showed the most abundant diversity. The level of diversity distributed symmetrically with radial direction from the center of the aging oil sludge spot. Over the distance of 100 m from the center, bacterial community diversity tends to be monotonous, with small differences especially in the horizontal direction underground. The alpha-diversity indicators also showed that the bacterial diversity of samples were close under the aging oil sludge. In addition, the aging oil sludge inhibited the growth of bacteria compared with the referenced unpolluted soil sample and also increased the diversities of soil bacteria. At the phylum level, the Proteobacteria, Chloroflexi, and Actinobacteria existing in the aging oil sludge-contaminated wetland soil constituted a larger proportion of the community, while the proportion of Firmicute was relatively less. On the contrary, Firmicute showed the highest content of 63.8% in the referenced soil. Under the genus level and family level, the corresponding strains that resisted the aging oil sludge were selected. According to the bacterial diversity analysis, the basic structure of the bacterial community which could be used for remediation of aging oil sludge-contaminated soil was also developed.
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20

Trimulono, Guntur, Lisa Lisdiana, Mahanani Tri Asri, M. Khoirul Rijal, and Hidayatul Lailiyyah. "Diversity of Bacterial Isolates in Water Mangrove Forest Wonorejo, Surabaya." MATEC Web of Conferences 372 (2022): 05011. http://dx.doi.org/10.1051/matecconf/202237205011.

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Plastic waste can be seen in several areas in the Wonorejo mangrove forest, Surabaya, which is also a habitat for various types of microbes. Research on bacterial isolates from water samples in mangrove forests needs to be conducted to determine their diversity. This research was conducted to determine the diversity and dominance of bacterial isolates in mangrove forest waters. Each water sample was taken from a site that is regularly irrigated (station 1) and a site that is flooded (station 2). The number of bacteria in mangrove forest water samples was determined using the Total Plate Count (TPC) method and bacterial isolation was performed using the pour plate method. Subsequently, the bacterial isolates were characterized based on their colonies and observed for their dominance. The number of bacteria at station 1 was 4.85x102CFU/mL and 2.55x105 CFU/mL at station 2. Both stations showed bacterial diversity. However, several bacterial isolates with the same character can be found in both stations. Further research should be conducted to determine the potential of these bacterial isolates as plastic-degrading agents.
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Oliveira, João Tiago Correia, Everthon Fernandes Figueredo, Williane Patrícia da Silva Diniz, Lucianne Ferreira Paes de Oliveira, Pedro Avelino Maia de Andrade, Fernando Dini Andreote, Júlia Kuklinsky-Sobral, Danúbia Ramos de Lima, and Fernando José Freire. "Diazotrophic Bacterial Community of Degraded Pastures." Applied and Environmental Soil Science 2017 (2017): 1–10. http://dx.doi.org/10.1155/2017/2561428.

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Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots ofBrachiaria decumbensStapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE) of thenifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR) technique. The increase in the degradation stage of theB. decumbensStapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated withB. decumbensStapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.
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22

Filée, J., P. Siguier, and M. Chandler. "Insertion Sequence Diversity in Archaea." Microbiology and Molecular Biology Reviews 71, no. 1 (March 2007): 121–57. http://dx.doi.org/10.1128/mmbr.00031-06.

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SUMMARY Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr ), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.
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23

Carson, Jennifer K., Vanesa Gonzalez-Quiñones, Daniel V. Murphy, Christoph Hinz, Jeremy A. Shaw, and Deirdre B. Gleeson. "Low Pore Connectivity Increases Bacterial Diversity in Soil." Applied and Environmental Microbiology 76, no. 12 (April 23, 2010): 3936–42. http://dx.doi.org/10.1128/aem.03085-09.

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ABSTRACTOne of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P< 0.012), but they were not affected by texture (P> 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P< 0.001) and was correlated with WFPS (sum of squared correlations [δ2] = 0.88,P< 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.
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Franco, Nelson Rivera, Miguel Ángel Giraldo, Diana López-Alvarez, Jenny Johana Gallo-Franco, Luisa F. Dueñas, Vladimir Puentes, and Andrés Castillo. "Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea." Diversity 13, no. 1 (December 31, 2020): 10. http://dx.doi.org/10.3390/d13010010.

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Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and diversity of six samples collected at different depths (1681 to 2409 m) in two localities (CCS_A and CCS_B). We found 1842 operational taxonomic units (OTUs) assigned to bacteria. The most abundant phylum was Proteobacteria (54.74%), followed by Bacteroidetes (24.36%) and Firmicutes (9.48%). Actinobacteria and Chloroflexi were also identified, but their dominance varied between samples. At the class-level, Alphaproteobacteria was most abundant (28.4%), followed by Gammaproteobacteria (24.44%) and Flavobacteria (16.97%). The results demonstrated that some bacteria were common to all sample sites, whereas other bacteria were unique to specific samples. The dominant species was Erythrobacter citreus, followed by Gramella sp. Overall, we found that, in deeper marine sediments (e.g., locality CCS_B), the bacterial alpha diversity decreased while the dominance of several genera increased; moreover, for locality CCS_A, our results suggest that the bacterial diversity could be associated with total organic carbon content. We conclude that physicochemical properties (e.g., organic matter content) create a unique environment and play an important role in shaping bacterial communities and their diversity.
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da Silva, Herculano, Tatiane M. P. Oliveira, and Maria Anice M. Sallum. "Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species." Genes 13, no. 11 (November 7, 2022): 2052. http://dx.doi.org/10.3390/genes13112052.

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Mosquitoes (Diptera: Culicidae) are found widely throughout the world. Several species can transmit pathogens to humans and other vertebrates. Mosquitoes harbor great amounts of bacteria, fungi, and viruses. The bacterial composition of the microbiota of these invertebrates is associated with several factors, such as larval habitat, environment, and species. Yet little is known about bacterial interaction networks in mosquitoes. This study investigates the bacterial communities of eight species of Culicidae collected in Vale do Ribeira (Southeastern São Paulo State) and verifies the bacterial interaction network in these species. Sequences of the 16S rRNA region from 111 mosquito samples were analyzed. Bacterial interaction networks were generated from Spearman correlation values. Proteobacteria was the predominant phylum in all species. Wolbachia was the predominant genus in Haemagogus leucocelaenus. Aedes scapularis, Aedes serratus, Psorophora ferox, and Haemagogus capricornii were the species that showed a greater number of bacterial interactions. Bacterial positive interactions were found in all mosquito species, whereas negative correlations were observed in Hg. leucocelaenus, Ae. scapularis, Ae. serratus, Ps. ferox, and Hg. capricornii. All bacterial interactions with Asaia and Wolbachia were negative in Aedes mosquitoes.
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LIANG, RONGRONG, XIAOQIAO YU, RENHUAN WANG, XIN LUO, YANWEI MAO, LIXIAN ZHU, and YIMIN ZHANG. "Bacterial Diversity and Spoilage-Related Microbiota Associated with Freshly Prepared Chicken Products under Aerobic Conditions at 4°C." Journal of Food Protection 75, no. 6 (June 1, 2012): 1057–62. http://dx.doi.org/10.4315/0362-028x.jfp-11-439.

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This study analyzed the bacterial diversity and spoilage-related microbiota associated with freshly prepared chicken products stored aerobically at 4°C, using “bone and chicken string,” a product popular in the People's Republic of China, as the study subject. Samples collected from three different factories were tray packaged with cling film and stored at 4°C. Bacterial diversity and dominant bacteria were analyzed using PCR amplification and denaturing gradient gel electrophoresis. Combined with selective cultivation of the dominant bacteria and correlation analysis, the dominant spoilage microbiota was determined. The results showed that bacterial diversity varied with different manufacturers. Such bacteria as Acinetobacter sp., Carnobacterium sp., Rahnella sp., Pseudomonas sp., Brochothrix sp., and Weissella sp. were detected in freshly prepared chicken products during storage. And Carnobacterium sp., Pseudomonas sp., and Brochothrix sp. bacteria were the common dominant spoilage bacteria groups in most freshly prepared chicken products from different factories. Carnobacterium was, for the first time, shown to be an important contributor to the spoilage-related microflora of freshly prepared chicken products stored aerobically under refrigeration. Our work shows the bacterial diversity and dominant spoilage microbiota of freshly prepared chicken products stored aerobically under refrigeration.
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Becker, C. G., A. V. Longo, C. F. B. Haddad, and K. R. Zamudio. "Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome." Proceedings of the Royal Society B: Biological Sciences 284, no. 1861 (August 23, 2017): 20170582. http://dx.doi.org/10.1098/rspb.2017.0582.

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Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus Batrachochytrium dendrobatidis ( Bd ) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats. Bd infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and Bd loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from Bd infection, we also evaluated the bi-directional microbiome- Bd link but failed to find a significant effect of skin bacterial diversity reducing Bd infections. Although weak, we found support for Bd increasing bacterial diversity and/or for core bacteria dominance reducing Bd loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host–pathogen–microbiome triangle.
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Bell, Jennifer K., Bobbi Helgason, and Steven D. Siciliano. "Brassica napus phyllosphere bacterial composition changes with growth stage." Plant and Soil 464, no. 1-2 (April 29, 2021): 501–16. http://dx.doi.org/10.1007/s11104-021-04965-2.

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Abstract Aims Phyllosphere bacteria play critical roles in plant growth promotion, disease suppression and global nutrient cycling but remain understudied. Methods In this project, we examined the bacterial community on the phyllosphere of eight diverse lines of Brassica napus for ten weeks in Saskatoon, Saskatchewan Canada. Results The bacterial community was shaped largely by plant growth stage with distinct communities present before and after flowering. Bacterial diversity before flowering had 111 core members with high functional potential, with the peak of diversity being reached during flowering. After flowering, bacterial diversity dropped quickly and sharply to 16 members of the core community, suggesting that the plant did not support the same functional potential anymore. B. napus line had little effect on the larger community, but appeared to have more of an effect on the rare bacteria. Conclusions Our work suggests that the dominant bacterial community is driven by plant growth stage, whereas differences in plant line seemed to affect rare bacteria. The role of these rare bacteria in plant health remains unresolved.
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Flores-Rivas, Cintia, Fernando Hernández-Quiroz, Loan Edel Villalobos-Flores, Alberto Piña-Escobedo, Alejandra Chavez-Carbajal, Khemlal Nirmalkar, and Jaime García-Mena. "Characterization of the Food Microbiota in Ready-to-Eat Mexican Foods." Proceedings 66, no. 1 (January 12, 2021): 32. http://dx.doi.org/10.3390/proceedings2020066032.

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Ready-to-eat food microbiota are the microorganisms present in the dishes that are currently consumed during meals. These microorganisms include those that may have a health benefit, are potentially pathogenic or have not yet been given a function. Foods suitable for consumption are not free of microorganisms; however, within the food industry only yeasts have been given a beneficial function, while other microorganisms such as filamentous fungi and bacteria have been studied for their negative effects on food. We determined the bacterial diversity in samples of highly demanded, freshly prepared, unspoiled ready-to-eat dishes by high-throughput DNA sequencing of 16S rDNA libraries. We found a great bacterial diversity, whereby the most abundant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, TM7 and Thermi, among others. These phyla included bacteria with remarkable abundances in some dishes. The alfa diversity analyses showed that the main dishes had the largest diversity. The beta-diversity analyses clustered the bacterial communities of soups, side plates, desserts, and beverages, and some main dishes. Based on our results we conclude that unspoiled ready-to-eat Mexican dishes contain a rich bacterial diversity, which may contribute to the organoleptic properties of the dishes without representing a sanitary risk for the consumers.
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Kanzaki, Yoshiaki, and Kazuhiro Takemoto. "Diversity of Dominant Soil Bacteria Increases with Warming Velocity at the Global Scale." Diversity 13, no. 3 (March 12, 2021): 120. http://dx.doi.org/10.3390/d13030120.

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Understanding global soil bacterial diversity is important because of its role in maintaining a healthy global ecosystem. Given the effects of environmental changes (e.g., warming and human impact) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated at the global scale to date. Thus, in this study, we focused on the dominant soil bacteria, which are likely critical drivers of key soil processes worldwide, and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects of warming velocity and human activities, while statistically controlling for the potentially confounding effects of current climate and geographic parameters with global climate and geographic data. We demonstrated that the diversity of the dominant soil bacteria was influenced globally, not only by the aridity index (dryness) and pH but also by warming velocity from the Last Glacial Maximum (21,000 years ago) to the present, showing significant increases. The increase in bacterial diversity with warming velocity was particularly significant in forests and grasslands. An effect of human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.
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Bali, Rana, Jonathan Pineault, Pierre-Luc Chagnon, and Mohamed Hijri. "Fresh Compost Tea Application Does Not Change Rhizosphere Soil Bacterial Community Structure, and Has No Effects on Soybean Growth or Yield." Plants 10, no. 8 (August 10, 2021): 1638. http://dx.doi.org/10.3390/plants10081638.

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Soil bacteria drive key ecosystem functions, including nutrient mobilization, soil aggregation and crop bioprotection against pathogens. Bacterial diversity is thus considered a key component of soil health. Conventional agriculture reduces bacterial diversity in many ways. Compost tea has been suggested as a bioinoculant that may restore bacterial community diversity and promote crop performance under conventional agriculture. Here, we conducted a field experiment to test this hypothesis in a soybean-maize rotation. Compost tea application had no influence on bacterial diversity or community structure. Plant growth and yield were also unresponsive to compost tea application. Combined, our results suggest that our compost tea bacteria did not thrive in the soil, and that the positive impacts of compost tea applications reported elsewhere may be caused by different microbial groups (e.g., fungi, protists and nematodes) or by abiotic effects on soil (e.g., contribution of nutrients and dissolved organic matter). Further investigations are needed to elucidate the mechanisms through which compost tea influences crop performance.
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Fang, Min, Robert J. Kremer, Peter P. Motavalli, and Georgia Davis. "Bacterial Diversity in Rhizospheres of Nontransgenic and Transgenic Corn." Applied and Environmental Microbiology 71, no. 7 (July 2005): 4132–36. http://dx.doi.org/10.1128/aem.71.7.4132-4136.2005.

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ABSTRACT Bacterial diversity in transgenic and nontransgenic corn rhizospheres was determined. In greenhouse and field studies, metabolic profiling and molecular analysis of 16S rRNAs differentiated bacterial communities among soil textures but not between corn varieties. We conclude that bacteria in corn rhizospheres are affected more by soil texture than by cultivation of transgenic varieties.
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Gumerov, Vadim M., Ekaterina P. Andrianova, and Igor B. Zhulin. "Diversity of bacterial chemosensory systems." Current Opinion in Microbiology 61 (June 2021): 42–50. http://dx.doi.org/10.1016/j.mib.2021.01.016.

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Söhngen, Carola, Boyke Bunk, Adam Podstawka, Dorothea Gleim, and Jörg Overmann. "BacDive—the Bacterial Diversity Metadatabase." Nucleic Acids Research 42, no. D1 (November 7, 2013): D592—D599. http://dx.doi.org/10.1093/nar/gkt1058.

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Lozupone, C. A., and R. Knight. "Global patterns in bacterial diversity." Proceedings of the National Academy of Sciences 104, no. 27 (June 25, 2007): 11436–40. http://dx.doi.org/10.1073/pnas.0611525104.

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Marchini, L., M. S. Campos, A. M. Silva, L. C. Paulino, and F. G. Nobrega. "Bacterial diversity in aphthous ulcers." Oral Microbiology and Immunology 22, no. 4 (August 2007): 225–31. http://dx.doi.org/10.1111/j.1399-302x.2006.00345.x.

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37

Steinbüchel, Alexander, and Henry E. Valentin. "Diversity of bacterial polyhydroxyalkanoic acids." FEMS Microbiology Letters 128, no. 3 (May 1995): 219–28. http://dx.doi.org/10.1111/j.1574-6968.1995.tb07528.x.

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Martínez-Romero, Esperanza, and JesúS Caballero-Mellado. "RhizobiumPhylogenies and Bacterial Genetic Diversity." Critical Reviews in Plant Sciences 15, no. 2 (January 1996): 113–40. http://dx.doi.org/10.1080/07352689.1996.10393183.

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Kirkup, Benjamin C. "Bacterial Strain Diversity Within Wounds." Advances in Wound Care 4, no. 1 (January 2015): 12–23. http://dx.doi.org/10.1089/wound.2014.0560.

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Ozyamak, Ertan, Justin M. Kollman, and Arash Komeili. "Bacterial Actins and Their Diversity." Biochemistry 52, no. 40 (September 24, 2013): 6928–39. http://dx.doi.org/10.1021/bi4010792.

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41

Low, David. "A mouthful of bacterial diversity." Trends in Microbiology 8, no. 3 (March 2000): 109. http://dx.doi.org/10.1016/s0966-842x(00)01711-x.

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Konhauser, Kurt O. "Diversity of bacterial iron mineralization." Earth-Science Reviews 43, no. 3-4 (May 1998): 91–121. http://dx.doi.org/10.1016/s0012-8252(97)00036-6.

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Yang, Wen, and Ariane Briegel. "Diversity of Bacterial Chemosensory Arrays." Trends in Microbiology 28, no. 1 (January 2020): 68–80. http://dx.doi.org/10.1016/j.tim.2019.08.002.

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Thomas, Christopher M. "Bacterial diversity and the environment." Trends in Biotechnology 14, no. 9 (September 1996): 327–29. http://dx.doi.org/10.1016/0167-7799(96)30023-1.

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Hochman, Ayala, and Iris Goldberg. "The diversity of bacterial catalases." Free Radical Biology and Medicine 9 (January 1990): 131. http://dx.doi.org/10.1016/0891-5849(90)90641-u.

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Zhang, Li, and Zhihong Xu. "Assessing bacterial diversity in soil." Journal of Soils and Sediments 8, no. 6 (October 17, 2008): 379–88. http://dx.doi.org/10.1007/s11368-008-0043-z.

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Eisenhauer, Nico, Stefan Scheu, and Alexandre Jousset. "Bacterial Diversity Stabilizes Community Productivity." PLoS ONE 7, no. 3 (March 28, 2012): e34517. http://dx.doi.org/10.1371/journal.pone.0034517.

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48

Ouwerkerk, D., and A. V. Klieve. "Bacterial Diversity within Feedlot Manure." Anaerobe 7, no. 2 (April 2001): 59–66. http://dx.doi.org/10.1006/anae.2001.0373.

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Steinbüchel, A. "Diversity of bacterial polyhydroxyalkanoic acids." FEMS Microbiology Letters 128, no. 3 (May 15, 1995): 219–28. http://dx.doi.org/10.1016/0378-1097(95)00125-o.

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Tamilarasan, G., M. Arumugam Pillai, and R. Kannan S. Merina Prem Kumari. "Genetic Diversity Studies in Rice for Bacterial Leaf Blight Resistance." International Journal of Trend in Scientific Research and Development Volume-2, Issue-5 (August 31, 2018): 797–806. http://dx.doi.org/10.31142/ijtsrd15915.

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