Comparative Analysis Of Bacterial Communities Research Articles

Comparative analysis of bacterial communities in the sediment and seawater environments from marine large yellow croaker cages (Zhejiang coast, China)

Bacterial community plays a vital role in the open-oceanic aquaculture ecosystem, and its stability is crucial for maintaining the health of mariculture fish. However, there are no reported studies on microbial communities in the culture environment of marine fish cages. In this study, bacterial community composition and diversity of seawater and sediment habitats from 5 large yellow croaker cage farms were first investigated by 16S rRNA-based high-throughput sequencing. The composition of bacterial communities was visualized at the phylum and genus levels. Meanwhile, biological and ecological functions were also predicted. The bacterial diversity observed at 3 inshore sampling sites was higher in seawater groups than that in sediment groups. The alpha diversity indices were influenced by the geographic location, especially the inshore site Yueqing (YQ), showing higher values than other sampling sites. The pathogenic bacteria were prevalent in the aquaculture environments, and probiotics showed a relatively low proportion by comparing the potential pathogens. Our study provides baseline data on bacterial communities and diversity in the open-oceanic environments of cage-culture large yellow croaker.

Effects of Algae on the Formation of Black Blooms and Bacterial Community Structure Changes in Sediments and Black Floats

Black bloom is a phenomenon of serious deterioration in shallow-water ecosystems worldwide. This study investigated the effects of algae on the formation of black blooms and the changes of the bacterial community using nearly in-situ cores for a 40-day indoor simulation. We designed experiments with different combinations of water (W), sediments-water (SW), and sediments-water-algae (SWA), and made a comparative analysis of bacterial communities in sediments and black floats. The results demonstrated that the severity of black blooms was considerably affected by the presence of cyanobacteria. The concentration of total nitrates (TN) and NH4+-N in the SWA group increased to 25.1 and 22.47 mg/L (4.05 and 5.5 times of their initial concentrations), respectively. The abundance of microorganisms in the sediments was significantly higher than that of the black floats. The dominant species in both sediments were Proteobacteria and Chloroflexi, whose total proportion exceeded 50%. The addition of algae did not change the dominant community of the sediments. In black floats, the dominant species of the SW group were Proteobacteria (39%) and Actinobacteria (16%), and these of the SWA group were Proteobacteria (38%) and Cyanobacteria (35%). The dominant species in black floats changed significantly. Cyanobacteria increased remarkably in black floats in the group of algae additions. The possible reason may be that the Actinobacteria were suppressed by Cyanobacteria. Therefore, the addition of algae has a significant promoting effect on black blooms and significantly affects the microbial community structure of black floats.

Comparative Analysis of Bacterial Communities and Their Functional Genes Under Low and Moderate Rice-Sodic Soils

Comparative Analysis of Bacterial Communities and Their Functional Genes Under Low and Moderate Rice-Sodic Soils

Comparative analysis of bacterial communities of water and intestines of silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) reared in aquaculture pond systems

Silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) are the most common filter-feeding fish species. Distinct niches of these two species lead to differences in their ecological function. Here, high-throughput sequencing of 16S rRNA gene was employed to investigate and compare the bacterial community and potential function of silver carp and bighead carp reared in aquaculture pond systems. We found no significant difference in alpha diversity between microbial community of water body and intestinal microbiota of silver carp and bighead carp. Bacterial community richness of bighead carp, however, was higher than that of silver carp. A significant separation between microbial community of water body and of two fish species was observed. The Norank_o__PeM15, norank_f__Alcaligenaceae and unclassified_p__Firmicutes were higher for bighead carp but only Pseudomonas was higher for silver carp. Compared with bighead carp, intestinal microbiota of silver carp also had less typical planktonic bacteria. A separation but non-significant of bacterial community between silver carp and bighead carp was observed. In terms of predicted community function for water body, except for the lower abundance of cell motility than silver carp, the other pathways were generally more enriched than the two fish species. For the comparison between silver carp and bighead carp, most metabolic pathways, e.g., nutrients transport and metabolism, were generally more enriched for silver carp. The results of this study gain a better appreciation of gut microbiome ecology relating to pond culture of two species of microphagic filter-feeding carps, which could be effectively used in the management of these two species to enhance production and health.

Comparative Analysis of Bacterial Communities in Lutzomyia ayacuchensis Populations with Different Vector Competence to Leishmania Parasites in Ecuador and Peru.

Differences in the gut microbial content of Lutzomyia (Lu.) ayacuchensis, a primary vector of Andean-type cutaneous leishmaniasis in Ecuador and Peru, may influence the susceptibility of these sand flies to infection by Leishmania. As a first step toward addressing this hypothesis, a comparative analysis of bacterial and fungal compositions from Lu. ayacuchensis populations with differential susceptibilities to Leishmania was performed. Bacterial 16S rRNA gene amplification and Illumina MiSeq sequencing approaches were used to characterize the bacterial composition in wild-caught populations from the Andean areas of Ecuador and southern Peru at which the sand fly species transmit Leishmania (Leishmania) mexicana and Leishmania (Viannia) peruviana, respectively, and a population from the northern Peruvian Andes at which the transmission of Leishmania by Lu. ayacuchensis has not been reported. In the present study, 59 genera were identified, 21 of which were widely identified and comprised more than 95% of all bacteria. Of the 21 dominant bacterial genera identified in the sand flies collected, 10 genera had never been detected in field sand flies. The Ecuador and southern Peru populations each comprised individuals of particular genera, while overlap was clearly observed between microbes isolated from different sites, such as the number of soil organisms. Similarly, Corynebacterium and Micrococcus were slightly more dominant bacterial genera in the southern Peru population, while Ochrobactrum was the most frequently isolated from other populations. On the other hand, fungi were only found in the southern Peru population and dominated by the Papiliotrema genus. These results suggest that variation in the insect gut microbiota may be elucidated by the ecological diversity of sand flies in Peru and Ecuador, which may influence susceptibility to Leishmania infection. The present study provides key insights for understanding the role of the microbiota during the course of L. (L.) mexicana and L. (V.) peruviana infections in this important vector.

Organic farming practices utilizing spent microbial biomass from an industrial fermentation facility promote transition to copiotrophic soil communities.

Organic farming has become more prevalent in recent years as consumer demand for organic food and fiber has rapidly grown. Until recently, organic fertilizers and soil amendments have largely been based on the practices of returning crop residues, manures and related agricultural wastes back to crop production areas. One rapidly growing segment in commercial organic fertilizer development is the use of spent microbial biomass (SMB) from industrial fermentation processes. While SMB is widely accepted in many organic farming systems (OFS), little is known concerning the effectiveness, environmental impact, and influence on prokaryotic communities in soils receiving this treatment. In this study, a comparative analysis of bacterial communities associated with OFS and conventional farming systems was performed over a growing season for a field containing yellow dent corn (Zea mays). A statistically significant increase in microbial population α-diversity, along with a strong recruitment of Proteobacteria and Actinobacteria populations, was observed in soils treated with SMB when compared to areas in the field that utilized conventional farmer practices. These phyla are members of the copiotrophic subgroup, and considered a signature for the use of traditional organic fertilizers. These results provide valuable new information that SMB functions similarly to traditional organic fertilizers in promoting a high level of functional prokaryotic diversity and plant growth-promoting bacteria, but in contrast do not contribute directly to viable microorganisms in the soil due to the sterilization of SMB prior to land application.

Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea.

Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.

Comparative Analysis of Bacterial Communities Associated with Healthy and Inflamed Peri-implant Tissues

Dental implants are used to restore dentition defects. However, despite the high efficiency of the method of placing dental implants, their integration can be accompanied by peri-implant diseases (peri-implant mucositis and peri-implantitis), which are inflammatory reactions induced by the bacterial activity. In the present pilot study, we described and compared the bacterial communities associated with healthy and inflamed peri-implant mucosal tissues using 16S rRNA gene amplicon pyrosequencing approach. It was revealed that various representatives of the phyla Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria were found at significant levels in healthy and peri-implant mucositis sites but in different proportions. Furthermore, it was shown that the genus Fusobacterium was the only group present in higher proportions on inflamed tissues than on healthy tissues surrounding dental implants of all patients. In addition, unclassified Methylobacteriaceae and the genus Veillonella as well as some other phylotypes were present at higher levels in peri-implant mucositis sites of some patients. This study indicates that several microbial agents may play important roles during the development of oral peri-implant diseases.

Illumina high-throughput sequencing and comparative analysis of bacterial communities in cherry orchard soil

ABSTRACTMicrobial diversity in the rhizosphere is affected by soil physical and chemical properties, which may be determined by plant species and growth stage. Exploring the bacterial communities in cherry rhizospheres may help in monitoring and conservation of soil quality. The aim of this study was to characterize the bacterial community structure between bulk soil and rhizosphere, using Illumina pyrosequencing of bacterial 16S rRNA genes, to determine the effect of soil types and seasons on bacterial diversity in cherry orchard. Sequences of 199,615 (30,162–35,399/sample) genes were obtained. Rhizosphere communities shared features with the surrounding bulk soil, such as predominance of Proteobacteria, Acidobacteria, and Actinobacteria. The relative abundance of certain bacterial lineages differed: Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were more abundant in the rhizosphere than in bulk soil. At the genus level, Burkholderia, Rhodococcus, Streptomyces, and Varivorax were more abundant in the rhizosphere, compared with the bulk. Specifically, Burkholderia and Rhodanobacter were abundant in the rhizosphere and bulk soil, respectively, and changed greatly with different growth stages. These results indicated that season variations and soil types affected the bacterial community composition in cherry orchard soil, which may have implications for understanding the status of cherry orchard nutrients in North China.

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata Reveals a Link among Alterations in Bacterial Holobiont Members, Anthropogenic Influence and Disease Outbreaks

Mass mortality events of benthic invertebrates in the Mediterranean Sea are becoming an increasing concern with catastrophic effects on the coastal marine environment. Sea surface temperature anomalies leading to physiological stress, starvation and microbial infections were identified as major factors triggering animal mortality. However the highest occurrence of mortality episodes in particular geographic areas and occasionally in low temperature deep environments suggest that other factors play a role as well. We conducted a comparative analysis of bacterial communities associated with the purple gorgonian Paramuricea clavata, one of the most affected species, collected at different geographic locations and depth, showing contrasting levels of anthropogenic disturbance and health status. Using massive parallel 16SrDNA gene pyrosequencing we showed that the bacterial community associated with healthy P. clavata in pristine locations was dominated by a single genus Endozoicomonas within the order Oceanospirillales which represented ∼90% of the overall bacterial community. P. clavata samples collected in human impacted areas and during disease events had higher bacterial diversity and abundance of disease-related bacteria, such as vibrios, than samples collected in pristine locations whilst showed a reduced dominance of Endozoicomonas spp. In contrast, bacterial symbionts exhibited remarkable stability in P. clavata collected both at euphotic and mesophotic depths in pristine locations suggesting that fluctuations in environmental parameters such as temperature have limited effect in structuring the bacterial holobiont. Interestingly the coral pathogen Vibrio coralliilyticus was not found on diseased corals collected during a deep mortality episode suggesting that neither temperature anomalies nor recognized microbial pathogens are solely sufficient to explain for the events. Overall our data suggest that anthropogenic influence may play a significant role in determining the coral health status by affecting the composition of the associated microbial community. Environmental stressful events and microbial infections may thus be superimposed to compromise immunity and trigger mortality outbreaks.

Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus

Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10-100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.

Comparing bacterial community fingerprints from white colonizations in Altamira Cave (Spain)

Monitoring bacterial communities is critical for assessing biodeterioration among other processes. This study presents a strategy and an example of comparative analysis of bacterial communities developing in a cave environment, Altamira Cave which contains unique paleolithic paintings. The analyzed question was whether white colonizations discovered throughout the cave corresponded to similar or different bacterial communities. Molecular fingerprints were obtained by PCR–DGGE from DNA and RNA and statistically compared. Results based on DNA analysis showed that a similar bacterial community was present in white colonizations throughout the cave. Fingerprints based on RNA confirmed the similarity of the major metabolically active components of these communities. The proposed procedure confirmed that white colonizations in Altamira Cave were a consequence of the development of a single complex bacterial community, and the method proves to be highly useful for comparative analysis of microbial communities, including biodeteriorating processes and any other comparative analysis of bacterial communities.

Phylogenetic Analysis of Bacterial Communities Associated with Larvae of the Atlantic Halibut Propose Succession from a Uniform Normal Flora

Halibut, the largest of all flatfishes is a valuable species with a great potential for aquaculture. Bacteria play an important role in regulating the health of the early life stages. The present article is the first broad-range molecular analysis of bacterial communities in larvae of the Atlantic halibut (Hippoglossus hippoglossus). DNA was extracted from larvae, water and silo biofilm from hatcheries in Norway, Scotland, Iceland and Canada. Eubacterial 16S rRNA gene fragments were amplified by polymerase chain reaction (PCR) with broad-range primers. Sequences spanning the hyper variable V3 region representing individual bacterial species were separated into community profiles by denaturing gradient gel electrophoresis (DGGE). The profiles revealed simple communities after hatching and bacterial succession following growth. Sequencing and phylogenetic analysis of excised DGGE bands suggested aerobic heterotrophs related to groups of Pseudomonas, Janthinobacterium and possibly Marinomonas to be the primary colonisers of the larvae. After onset of feeding, fermentative species (Vibrio) were detected as well. Comparative analysis of bacterial communities from different geographical regions indicated that larvae of the Atlantic halibut possess a distinct and specific normal flora.