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Bacterial Community Structure and Diversity of Closely Located Coastal Areas

Bacterial Community Structure and Diversity of Closely Located Coastal Areas

Abstract Bacterial community structure and diversity of two closely located stations are usually considered similar which can be verified by more intensive investigations using relatively large amount of datasets from the next generation sequencer. This study was conducted to assess the bacterial community structure and diversity between two closely located coastal stations, the port side and the sea side of the Oarai, Ibaraki, Japan from March 2013 to July 2014 using 454 GS Junior se- quencer. Two stations underwent similar changes in physicochemical properties but the commu- nity structure and diversity was different. The Proteobacteria (the class Alphaproteobacteria, fol- lowed by the Gammaproteobacteria) and the Bacteroidetes (the class Flavobacteriia) were two abundant phyla in both the stations. But, the Flavobacteriia was more abundant in the port side, contributed about 26% to 48%, compared to the sea side (about 12% to 39%). Conversely, the relative abundance of the Gammaproteobacteria was higher on the sea side, about 10% to 17%, compared to the port side (about 4% to 12%). Among others, the phyla Cyanobacteria, Deferri- bacteres, Verrucomicrobia and the class Betaproteobacteria were also relatively abundant at the sea side. Because of their dominancy, the class Flavobacteriia and Alphaproteobacteria were further analysed at a lower phylogenetic level and marked differences were observed between the stations.
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Study of the animal to animal variability in bacterial community structure in the goats' rumen

Study of the animal to animal variability in bacterial community structure in the goats' rumen

The trial was divided in 3 periods. In period I, three adult goats cannulated in the rumen were fed alfalfa hay at maintenance level (Prieto et al., 1990) for a month and then samples of rumen con- tents collected at 0, 2 and 4 hours after the morning feeding on days 31 (d1) and 45 (d2). To evalu- ate the consistency of differences amongst animals observed in Period I, 1.5 kg of rumen content were swapped between animals in two additional periods (II and III), during which animals were also fed alfalfa hay for one month and samples collected on days 31 (d1) and 45 (d2) 2 hours after the morning feeding. In Period II the content was transferred from animal 1 to 2, from 2 to 3 and from 3 to 1. In Period III the rumen content was transferred from animal 2 to 1, from 3 to 2 and from 1 to 3. Approximately 50 g of samples of rumen contents were freeze-dried and thoroughly mixed by physical disruption using a bead beater (Mini-bead Beater; BioSpec Products, Bartlesville, OK, USA) before DNA extraction, which was performed from approximately 50 mg sub-sample using the QIAamp® DNA Stool Mini Kit (Qiagen Ltd, West Sussex, UK) following the manufacturer’s instructions. DNA samples were used as templates for terminal restriction fragment length poly- morphism (t-RFLP) analysis (Hongogh et al., 2005) to study total bacterial community structure: PCR was performed using a 16S rRNA bacterial-specific primer pair, cyanine labelled 27F (5’- AGA GTT TGA TCC TGG CTG AG-3’) and unlabelled 1389R (5’-AGG GGG GGT GTG TAG AAG-3’). The PCR product was purified (Millipore MultiScreen® PCR-96 plate with 20 inches Hg vacuum). The DNA concentration within each sample was determined by spectrophotometry (Nanodrop® ND-1000 spectrophotometer) and then diluted to 20ng/µl. Restriction enzyme diges- tion was performed using HhaI at 0.25 U/µl. Analysis of terminal restriction fragments in samples was performed by using the Bray-Curtis distance between binary profiles (presence/ab sence of peaks) to construct dendrograms. Analysis of the T-RFLP peaks profiles was carried out by CAP 4 software (Pisces Conservation Ltd., Lymintong, Hampshire, UK).
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Spatial patterns in bacterial community structure and function within shallow alpine tarns

Spatial patterns in bacterial community structure and function within shallow alpine tarns

representing individual samples that did not fall within the main clusters. ......... 40 Figure 20. Similarity in bacterial community structure and function within the tarns. Bacterial community data for each tarn were subjected to a data reduction procedure by non-metric multidimensional scaling of Bray-Curtis similarity data. The differences between the highest and lowest 1-d configuration scores for each plot were then used to classify the configuration into ten equally sized classes. The bacterial community data falling within each class was assigned a different colour, across a gradient from dark blue (lowest 1-d configuration score) to light green (highest 1-d configuration score. The outcome of this approach is that samples hosting more similar bacterial
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Effects of Root Isoflavonoids and Hairy Root Transformation on the Soybean Rhizosphere Bacterial Community Structure

Effects of Root Isoflavonoids and Hairy Root Transformation on the Soybean Rhizosphere Bacterial Community Structure

multiple species (Fakruddin and Mannan, 2013). Such factors make detailed microbial community analysis difficult. To achieve a more in-depth analysis, many of the aforementioned rhizosphere studies also implemented pyrosequencing. This technique is particularly useful since it can process long read lengths with high accuracy, although it suffers from a high error rate when encountering poly-bases longer than 6 base pairs (Liu et al., 2012). For this study, we chose to first use DGGE to detect large shifts in the rhizosphere bacterial community structure. DGGE was chosen over techniques like FISH since our focus was on the bacterial community rather than a few target species. To limit PCR amplification bias, we stopped the process while sequence amplification was in the log phase. We then used
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Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system

(2011) Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.. The copyright exception in section 29 of[r]

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The Impact of Colonizer Plants on Bacterial Community Structure and Function in Early Successional Soils of a Glacial Forefield

The Impact of Colonizer Plants on Bacterial Community Structure and Function in Early Successional Soils of a Glacial Forefield

2008). Further work at the Dama glacier by Brankatschk et al. (2010) found that nifH gene copy abundances peak in early successional soils with the presence of the first plant patches. This suggests that ecologically important interactions between initial plant colonizers and bacterial community structure and function occur at the intersection of the unvegetated and vegetated landscapes; however, questions remain about the biotic and abiotic factors structuring microbial communities. In this study, I focused on plant-microbe interactions at this transitional

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Host species identity, site and time drive temperate tree phyllosphere bacterial community structure

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure

Consistent with the idea of environmental selective pressure on phyllosphere communities due to abiotic conditions such as temperature and precipitation, cli- mate differences between sites (monthly precipitation and mean monthly temperature) were correlated with variation in phyllosphere bacterial community structure. In addition, the effect of sampling time and the inter- action between sampling time and site on phyllosphere community structure suggests that phyllosphere com- munities undergo a succession during the growing sea- son. As previously demonstrated for individual host tree species by Redford and Fierer [25] for bacterial commu- nities and by Jumpponen and Jones [7] for fungal com- munities, leaf communities were temporally dynamic. However, the variance explained by sampling time was small relative to the importance of host species and site, suggesting that once a community of bacteria success- fully colonizes a leaf, temporal changes are not enough to overcome the influence of host species identity and site on community assembly. In the temperate forest we studied, growing season had a significant impact on
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Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant

Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant

We assessed differences in bacterial community structure among Native, Gulf, and Introduced P. australis lineages using Adonis, which is a PERMANOVA 63 implemented in QIIME, with signi fi cance assessed at an alpha of 0.01. We assessed changes in community structure with distance by plotting the pairwise Bray–Curtis dissimilarity coefficient against pairwise distance between locations and calculated the linear regression between the two in R. We used PiCrust 64 , which assigns function based on 16S rRNA marker sequences using an ancestral state reconstruction approach, to determine bacterial metabolisms. To assess differences in potential bacterial metabolisms among lineages, we implemented PiCrust on Galaxy 64–66 , using closed-reference OTU picking in QIIME. The resulting biom fi le was uploaded to Galaxy (http://huttenhower.sph.harvard.edu/galaxy/) and data were normalized to account for multiple copies of 16S rRNA in some bacteria.
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Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Received Date: 14 November 2017 Revised Date: 16 December 2017 Accepted Date: 27 December 2017 Please cite this article as: Lin, Z., Zhen, Z., Ren, L., Yang, J., Luo, C., Zhong, L., Hu, H., Zhang, Y., Li, Y., Zhang, D., Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil, Chemosphere (2018), doi: 10.1016/

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Bacteriophages with potential for inactivation of fish pathogenic bacteria: survival, host specificity and effect on bacterial community structure

Bacteriophages with potential for inactivation of fish pathogenic bacteria: survival, host specificity and effect on bacterial community structure

Received: 22 September 2011; in revised form: 21 October 2011 / Accepted: 28 October 2011 / Published: 7 November 2011 Abstract: Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.
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Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F–1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degrada- tion of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.
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Influence of vegetation on sediment bacterial community structure, microbial enzyme activities and phosphorus retention in constructed freshwater wetlands

Influence of vegetation on sediment bacterial community structure, microbial enzyme activities and phosphorus retention in constructed freshwater wetlands

10 freshwater wetland plants at the Field Station, a list of understory vegetation and associated habitats was compiled (Menon and Holland, submitted to Castanea). Wetland plants are known to remove 52-67% of influent phosphorus (Busnardo 1992, McJannet et al. 1995), and the right selection of plants is necessary for maintaining and improving the effectiveness of constructed wetlands (McJannet et al. 1995). The objectives of the co-operative agreement between USDA-ARS-NSL Water Quality Ecology Unit and the University of Mississippi are to conduct research on the use of plants and wetland ecosystems to reduce agricultural contaminants, to better understand the causes of aquatic impairments, and to provide recommendations for contaminant reduction. There is little quantitative information available comparing the growth characteristics and treatment performance of various plants in constructed wetland systems, effect of specific plant species on sediment microbial enzymes in phosphorus-loaded constructed wetlands, and bacterial community structure associated with the wetland plants.
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Changes in bacterial community structure in seawater mesocosms differing in their nutrient status

Changes in bacterial community structure in seawater mesocosms differing in their nutrient status

If we accept that the larger the cells, the higher their productivity, the selection of large bacteria may result in the selection of a few very active and productive cel[r]

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Assessment of the bacterial community structure in a Brazilian clay soil treated with atrazine

Assessment of the bacterial community structure in a Brazilian clay soil treated with atrazine

Several microorganisms able to remove atrazine from soil by degrading it have been enriched and isolated (Ralebitso et al. 2002; Singh et al. 2004; Piutti et al. 2003; Rhine et al. 2003; Vaishampayan et al. 2007; Getenga et al. 2009). However, the occurrence of bacterial populations able to remove atrazine does not exclude that chronic contamination can negatively affect the most sensitive natural populations and consequently decrease bacterial diversity and to some extent ecosystem functioning. The maintaining of biodiversity is particularly important in Brazilian soil ecosystems, which contain a wide and well-known diversity of flora and fauna, although knowledge about the microbial communities is quite scarce (Faoro et al. 2010). Pollution and intensive cultivation of agricultural land may influence soil quality and productivity, but little is known of their effects on soil microbial commu- nities, and the consequent impacts on soil functioning.
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Effects of organic fertilization on soil bacterial community structure in incubated microcosms

Effects of organic fertilization on soil bacterial community structure in incubated microcosms

ABSTRACT Addressing the growing demand for food from a burgeoning population requires agricultural methods that sustainably support increases in crop production while maintaining environmental health. Agricultural practices that include the use of compost, in lieu of mineral fertilizers, have been shown to reduce environmental impacts and improve soil health. Producers seeking to improve sustainability through compost use are challenged by the chemical form and availability of nutrients in organic amendments, limiting their ability to predict when nutrients will be available to crops. To better understand nutrient dynamics in soils amended with organic fertilizers, we compared the soil microbial community response to amendments with differing carbon and nitrogen content. Composted horse manure was chosen to represent an organic high carbon amendment, and alfalfa hay was chosen to represent a high nitrogen amendment.
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Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

utilization in the rumen is compensated for by increased post- ruminal digestion. This might explain why no differences are observed in whole tract feed digestion, even though there might be differences in microbial populations in the rumen causing differences in digestibility. On the other hand, feed efficiency studies have shown differences in microbial structure between animals in which feed utilization for production of meat or milk also differed ( Guan et al., 2008; Zhou et al., 2009; Shabat et al., 2016 ). In the study by Guan et al. (2008) , microbial community profiles from feed-efficient steers were clustered together and differed from those in inefficient steers, showing that the different microbial community related to lowered feed efficiency in rumen was not totally compensated with higher post ruminal digestion. In the recent study by Shabat et al. (2016) feed efficient cows had lower richness in both microbiome- and gene content compared
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Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

The overall close similarity of the CE-SSCP fingerprints, each represented by 13–24 ribotypes, indicate that the bac- terial community structure in the surface microlayer strongly resembles that in surface waters. Even though the probes we used in the present study provide information on a low phylo- genetic level, the results from the in situ hybridization appear to support this conclusion. Given the low bacterial growth rates determined in the present study, and the relatively short time period over which the surface microlayer persists, an in situ development of a specific bacterioneuston community is unlikely. Physical processes are mainly responsible for the formation of the surface microlayer, with upward transport of particulate material being a predominant process. The dif- ferences that we observed in the fingerprints between the two layers is most likely owing to the selective enrichment of the surface microlayer by specific ribotypes. Likely candidates are bacteria attached to particles that are transported to the air-sea interface. The structure of the bacterial community attached to particles in the water column differs from that of free-living bacteria (Acinas et al., 1999; Riemann and Wind- ing, 2001; Ghiglione et al., 2007) and Bacteroidetes were found to have an important contribution to the bacterial com- munities associated with aggregates (DeLong et al., 1993;
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Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

Our results support previous findings showing that rural and urban microbial commu- nities differ in composition (6, 7, 78). The proportion of green spaces and species diversity have been suggested as potential drivers of these natural environment-urban environment differences in community composition (8), but our work shows that the plant-associated microbiota per se is different from what is usually found in the natural environment as described in previous work in the natural temperate forest (26, 27). Urban abiotic and biotic conditions linked directly and indirectly to human actions are potential drivers of the changes in leaf microbial community structure. Therefore, future studies comparing the relative influences of the increased stress, the sources of microbial input, and the host capacity to select their microbiota in urban settings on the plant-associated microbiome are required to identify clearly the causes of this shift in the urban plant microbiome. In particular, future greenhouse experiments characterizing the influence of physical lesion, nutrient deficiency, water limitation, and air contamination on the plant microbiome and plant fitness will provide key information to support the devel- opment of the management of the urban microbiome. Such studies have the potential of identifying the most effective interventions to manage the urban plant microbiome (i.e., increasing plant diversity, increasing plant cover, reducing heat islands, reducing air contamination, introducing specific plant species). Although this work focused on bacterial communities, leaf-inhabiting fungi, yeasts, bacteriophages, and small eu- karyotes could be impacted by the higher intensity of anthropogenic pressures but could also interact with tree leaf bacterial communities. Therefore, upcoming studies of the urban plant microbiome focusing on these organisms will definitely provide crucial information to the field, especially in considering the tree phyllosphere as a vector for the airborne microbiome. In addition, including an estimation of the leaf microbial load would allow future work to directly assess the quantitative effect of increased anthro- pogenic pressures on the phyllosphere microbiome. Finally, our work here also high- lights the importance of future studies aimed at understanding the impact of this microbial enrichment in tree leaf microbial communities on host tree health through pathogen infections and pest attacks.
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Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

In contrast, comparison of NEC and control patients demonstrates a distinct trajectory of community develop- ment in patients that develop NEC. The ultimate trajec- tory of microbiota in these infants does not overlap with that of control infants, suggesting that at crucial times a healthy trajectory can be misdirected towards deviant states (for example, NEC). The deviation from control appears to occur two to three weeks prior to NEC. Pre- vious work by others [14] had noted a similar deviation from healthy infants but only at one week prior to the on- set of NEC. Earlier detection, as demonstrated here, would provide an extended timeframe for intervention, but is also indicative of a more prolonged microbial community deviation prior to pathology emergence. Additionally, the earlier detection of this trajectory also led us to sequence metagenomes from earlier time points (three weeks prior to NEC diagnosis) and allowed the identification of func- tional gene sets that may contribute to the onset of NEC. The initial time point from the set of twins we sampled coincided with the two to three week transition period that we identified in the original control cohort (Figure 2). Although the 16S-based data indicate a shift between con- trols and those that go on to develop NEC, the first time point comparison between twins, based on ordination of the functional genes detected in the metagenomes does not reflect a major difference. This may be explained by organisms that differ at taxonomic resolutions finer than those reported here, occupying a similar ecological niche between patients at this first time point. In other words, there is a functional redundancy between the community memberships wherein different organisms can perform the same community function. Our present efforts are a coarse level description of functional differences between samples that will provide a candidate set of functions to investigate at a finer scale resolution in subsequent work.
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Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

However, in order to prove these observations statistically, an ordination analysis was applied, correlating the DGGE patterns with the environmental variables. Due to the low value of the first axis data distribution (1.459), the ordination method used was the redundancy analysis (RDA), which has ordinate the environmental variables in the following order of importance for the structuring of bacterial communities in the phyllosphere of mangroves: plant species > mangrove location. This ordination is also possible to be observed in the RDA plot (Figure 4), where the variance represented in the first axis indicates a strong effect of plant species in the community composition, mostly by the separation of R. mangle samples. In the second axis it is indicated the spatial effect on the community composition, although small overlap was observed for samples from distinct mangroves (Figure 4). These observations were corroborated by the Monte Carlo test (Table 1). However, the effect of the observed environmental variables could only explain a small part of the variation, as observed by the sum of λA.
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