Differences In Bacterial Community Composition Research Articles

Effects of temperature on Paramoeba perurans growth in culture and the associated microbial community.

Population growth, in vitro, of three Paramoeba perurans cultures, one polyclonal (G) and two clonal (B8, CE6, derived from G), previously shown to differ in virulence (B8 > G > CE6), was compared at 10 and 15 °C. B8 showed a significantly higher increase in attached and in suspended amoebae over time at 15 and 10 °C, respectively. CE6 and G also had significantly higher numbers of suspended amoebae at 10 °C compared with 15 °C at experiment termination. However, in contrast to B8, numbers of attached amoebae were significantly higher at 10 °C in CE6 but showed a similar trend in G at the end of the experiment. Numbers of both suspended and attached amoebae were lower in B8 compared with CE6 and G. Significant differences in bacterial community composition and/or relative abundances were found, between cultures, between temperatures and between the same culture with and without amoebae, based on 16S rRNA Illumina MiSeq sequencing. Bacterial diversity was lower in B8 and CE6 compared with G, possibly reflecting selection during clonal isolation. The results indicate that polyclonal P. perurans populations may contain amoebae displaying different growth dynamics. Further studies are required to determine if these differences are linked to differences seen in the bacterial communities.

Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants

Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples) and municipal wastewater treatment plants (mWWTPs) (27 samples) through meta-analysis based on 16S rRNA gene amplicon sequencing, and identified putatively important organisms and their ecological correlations. Non-metric multidimensional scaling indicated that the pWWTPs, iWWTPs and mWWTPs showed distinctive differences in bacterial community composition (P < 1e−04), and the pWWTPs had significantly lower bacterial diversity than the mWWTPs (P < 1e−06). Thermotogae and Synergistetes phyla only strictly dominated in the pWWTPs, and 26, 30 and 6 specific genera were identified in the pWWTPs, mWWTPs and iWWTPs, respectively. Totally, 15 and 1300 OTUs were identified as core and occasional groups, representing 23.2% and 66.2% of the total read abundance of the pWWTPs, respectively. Permutational multivariate analysis of variance revealed that the bacterial components were clearly clustered corresponding to the types of pharmaceutical wastewater, and a total of 129 local specific OTUs were identified in the pWWTPs, among which anticancer antibiotics pWWTPs had the highest number of specific OTUs (40 ones). Co-occurrence network revealed that the species dominating in the same type of pWWTPs tended to co-occur much more frequently than theoretical random expectation. The results may extend our knowledge regarding the ecological status and correlation of the key microflora in pWWTPs.

Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises.

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

Effects of experimental harvesting of an invasive hybrid cattail on wetland structure and function

Invasive plants, such as the hybrid cattail Typha × glauca, can reduce biodiversity and alter the ability of wetlands to provide critical ecosystem services, including nutrient cycling and carbon storage. Several approaches have been used to reduce Typha dominance and restore invaded wetlands, but long‐term studies assessing benefits of these restoration efforts are limited. A previous study demonstrated that aboveground harvesting of Typha × glauca stems and litter reduced Typha dominance 2 years post‐treatment in a Great Lakes coastal wetland. In the current study, we extended monitoring of experimental aboveground Typha harvest to 4 years post‐treatment and added assessments of treatment effects on soil nutrients, carbon emissions, and microbial community composition. Aboveground harvest treatment resulted in a dramatic reduction in Typha litter cover that persisted for 4 years, increased soil temperature, and increased abundance of the native plant genus Carex. However, aboveground harvest treatment did not significantly reduce Typha abundance, nor did it have significant effects on soil nutrient concentrations, carbon fluxes, or the taxonomic composition of soil microbial communities. We did observe differences in bacterial community composition between plots based on time since Typha invasion, which may indicate some legacy effects of Typha invasion. At the scale of this experiment (4 × 4 m plots), our results indicate that a single aboveground removal of Typha × glauca is not sufficient to restore a heavily invaded freshwater wetland ecosystem, and that periodic harvesting of Typha stems and litter may be required to maintain native plant abundance.

The bacterial community and local lymphocyte response are markedly different in patients with recurrent tonsillitis compared to obstructive sleep apnoea

IntroductionObstructive sleep apnea (OSA) is now a more common indication for tonsillectomy than recurrent tonsillitis (RT) [1,2]. Few studies have addressed possible differences in pathogenesis between these two conditions. Children with RT and OSA are often being treated in the community with multiple courses of antibiotics before surgery. Current understanding of the role of bacteria in disorders of the tonsils is mainly based on the culture of tonsil swabs. Swab cultures reflect only a very small fraction of the bacteria present on the mucosal surface and may not represent the bacterial communities within the tonsil crypts [3,4]. This study aimed to evaluate the local lymphocyte response and associations with bacterial community composition using molecular techniques of the tonsils removed from children for RT or OSA. MethodThe palatine tonsils were removed by extracapsular dissection from 24 patients with age range one to ten years, 14 of whom had RT and 10 had OSA. The fixed tonsil tissues were evaluated for bacteria by Gram-staining and presence of connective tissue by safranin staining. B lymphocytes and T lymphocytes were also measured immunohistochemically. Finally, previously published bacterial community data for this cohort were reassessed for associations with RT and OSA, and with the observed lymphocyte patterns. ResultsIn tonsils from patients with RT, large micro-colonies of bacteria were observed in the tonsil crypts, and a large number of B and T lymphocytes were noted immediately adjacent to the tonsil crypt itself. In marked contrast, the tonsils from patients with OSA had no bacteria identified, and no significant skewing of lymphocytes based on site (such as follicles or crypts). We observed that the majority of lymphocytes surrounding the bacterial micro-colonies were B lymphocytes with a mean ratio of 109:55 (B lymphocytes: T lymphocytes). Bacterial community diversity was not different between the two cohorts; however, there were significant differences in bacterial community composition. Children with RT had a higher relative abundance of members from the genera Parvimonas, Prevotella, and Treponema. While children with OSA had a higher relative abundance of Haemophilus, and Capnocytophaga. ConclusionThese results demonstrate significant differences in the local lymphocyte response and bacterial community composition in tonsil tissue between RT and OSA patients. It suggests that the response to antibiotics used in the treatment of these two conditions may be different. Furthermore, the presence of lymphocytes in RT within the tonsil crypt outside the tonsil epithelium is a unique observation of the location of these cells.

Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities.

Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.

Microbial community composition and methanogens’ biodiversity during a temperature shift in a methane fermentation chamber

ABSTRACTMore information on the connection between anaerobic digestion (AD) parameters and composition of the microbial community involved in the AD process is required to gain a better understanding of how a bioreactor functions. The aim of this study was to analyse the composition of microbial communities and the dynamics of methanogens’ biodiversity changes during the shift from mesophilic (38°C) to thermophilic (55°C) conditions during biogas production. The total microbial composition was examined via the metagenomic approach based on 16S rRNA gene sequencing, whereas the methanogen communities were analysed using PCR–DGGE (Polymerase Chain Reaction–Denaturing Gradient Gel Electrophoresis) of mcrA. Even though the temperature is one of the crucial parameters affecting microorganisms involved in the AD process, the results presented here revealed that there were no statistically significant differences in bacterial community composition between the mesophilic and thermophilic phases of the process. The most abundant phyla were found to be Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. However, the methanogens’ community genotypic structure as examined by the PCR–DGGE method changed under thermophilic conditions. The temperature had the strongest impact on the archaeal methanogens in the fermentation chamber directly after implementing the temperature shift. A relatively higher biogas yield and average content of CH4 in the produced biogas were observed under thermophilic conditions.

Strong associations between plant genotypes and bacterial communities in a natural salt marsh.

Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice‐daily flooding by tides, would serve as a particularly conservative test of the strength of plant–microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure. Within a salt marsh in the northeastern United States, we characterized genotypes of the foundational plant Spartina alterniflora using microsatellite markers, and bacterial metagenomes within marsh soil based on pyrosequencing. We found significant differences in bacterial community composition and diversity between bulk and rhizosphere soil, and that the structure of rhizosphere communities varied depending on the growth form of, and genetic variation within, the foundational plant S. alterniflora. Our results indicate that there are strong plant–microbial associations within a natural salt marsh, thereby contributing to a growing body of evidence for a relationship between plant genotypes and microbial communities from terrestrial ecosystems and suggest that principles of community genetics apply to this wetland type.

Bacterial metataxonomic profile and putative functional behavior associated with C and N cycle processes remain altered for decades after forest harvest

While the impacts of forest disturbance on soil physicochemical parameters and soil microbial ecology have been studied, their effects on microbial biogeochemical function are largely unknown, especially over longer time scales and at deeper soil depths. This study investigates how differing organic matter removal (OMR) intensities associated with timber harvest influence decadal-scale alterations in bacterial community composition and functional potential in the upper 1-m of the soil profile, 18 years post-harvest in a Pinus taeda L. forest of the southeastern USA. 16S rRNA amplicon sequencing was used in conjunction with soil chemical analyses to evaluate (i) treatment-induced differences in bacterial community composition, and (ii) potential relationships between those differences and soil biogeochemical properties. Furthermore, functional potential was assessed by using amplicon data to make metagenomic predictions. Results indicate that increasing OMR intensity leads to altered bacterial community composition and the relative abundance of dominant operational taxonomic units (OTUs) annotated to Burkholderia and Aciditerrimonas; however, no significant differences in dominant phyla were observed. Genes involved in nitrification were significantly lower in the most intensively harvested treatment, most likely as a result of reduced substrate. Additionally, the relative abundance of genes associated with dissimilatory nitrate reduction and denitrification were highest in the most intensively harvested plots, indicating that the volatilization of N was a potential pathway of N loss in that treatment. Genes associated with glycosyltransferases were significantly reduced with increasing harvest intensity while polysaccharide lyases increased. Additionally, when overall differences in N-cycling genes were observed (0–100 cm), they generally occurred at soil depths below 30 cm, indicating the importance of examining deeper soil horizons when assessing the effect of forest disturbance on soil biogeochemical processes.

Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

While sponges are generally known to host a wide range of microbial associates, the composition and specificity of the microbial communities in carnivorous sponges are poorly understood. We used 16S rRNA gene data to examine and compare the bacterial communities associated with distinct anatomical regions of two carnivorous sponge species, Chondrocladia grandis and Cladorhiza oxeata, sampled from Baffin Bay and the Gulf of Maine (C. grandis only). The two sponge species hosted distinct bacterial communities, with taxonomic diversity being greater in C. grandis. Some bacterial taxa (including particular oligotypes) were consistently recovered in multiple host individuals from geographically distant sites, suggesting specificity. Within C. grandis, certain bacterial taxa were enriched in particular anatomical regions, suggesting functional roles in carnivorous sponge metabolism or other biological processes. Stable isotope analysis provided no evidence for methanotrophy in the sponges examined, but Gulf of Maine C. grandis might incorporate 13C-depleted carbon via the bacteria-mediated heterotrophic degradation of other hydrocarbons. Overall, our results demonstrate that the carnivorous sponge microbiome appears host species specific and stable, even over large geographical areas. The observed differences in bacterial community composition and diversity between C. grandis and C. oxeata may reflect differences in trophic adaptability, specialization, and overall reliance on associated bacteria.

Bacterial Biofilm Communities and Coral Larvae Settlement at Different Levels of Anthropogenic Impact in the Spermonde Archipelago, Indonesia

Populations on small islands surrounded by coral reefs often heavily depend on the services provided by these reefs. The health and recovery of reefs are strongly influenced by recruitment of coral larvae. Their settlement relies on cues such as those emitted from bacterial communities forming biofilms on reef surfaces. Environmental conditions can change these bacterial community compositions (BCC) and may in turn affect settlement of coral larvae. At three small inhabited islands in the Spermonde Archipelago, Indonesia, with different distance from the mainland, BCC and coral recruitment were investigated on artificial ceramic tiles after 2-8 weeks exposure time and on natural reef substrate. Water parameters showed a clear separation between inshore and near-shore/mid-shelf sites, with distinct benthic communities at all three sites. No coral recruitment was observed at the inshore site with highest natural and anthropogenic stressors. At the other two sites coral recruitment occurred on natural surfaces (recruits per 100 cm2: 0.73 ± 1.75 near-shore, 0.90 ± 1.97 mid-shelf), but there was no significant difference between the two sites. On artificial substrates coral recruitment differed between these two sites, with tile orientation and with exposure time of the tiles in the reef. The most abundant bacteria on both substrates were Gammaproteobacteria, Alphaproteobacteria and Cyanobacteria. BCC was strongly correlated with water quality and significant differences in BCC between the inshore site and near-shore/mid-shelf were found. On artificial substrates there was a significant difference in BCC also with exposure time in the reef. Our study highlights the value of taking both BCC and coral recruitment into account, in addition to the environmental conditions, when considering the recovery potential of coral reefs.

Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors.

Microbiota associated with mosquito vector populations impact several traits of mosquitoes, including survival, reproduction, control, and immunity against pathogens. The influence of seasonal variations and mosquito species on mosquito gut microbiota is poorly understood. We sought to determine whether the mosquito microbiota associated with immature stages of two congeners (Culex coronator and Culex nigripalpus) differ temporally and between the two species. Using high throughput 16S rRNA gene sequence analysis, we characterized bacterial and archaeal communities found in the immature stages of the two Culex mosquito species sampled over three seasons to compare the diversity of bacteria between the two species. Beta diversity analyses of the larval microbiota sequences revealed that the two Culex species differed significantly, both temporally within each species and between the two species. Bacteria in Cx. coronator larvae were dominated by Alphaproteobacteria, mainly associated with Roseoccocus and unidentified species of Rhizobiales, and two unidentified species of Cyanobacteria. In contrast, Cx. nigripalpus was dominated by Thorsellia anophelis (Gammaproteobacteria), Clostridium, an unidentified species of Ruminococcacae (Clostridiales), and additional unidentified species associated with Erysipelotrichaceae (Erysipelotrichales), Bacteroidales, and Mollicutes. Results of our study revealed both seasonal and interspecies differences in bacterial community composition associated with the immature stages of Cx. coronator and Cx. nigripalpus vector populations in Florida. These results have important implications for our understanding of the underlying factors of variations in disease transmission among seasons, susceptibility to various pesticides, and other biotic factors, including the role of the microbiota on the spread of invasive species. In addition, our results suggest close associations of certain bacteria species with each of the two Culex species that will be further targeted for their potential in the development of microbial-based control strategies.

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake.

Although previous studies have compared the diversity and community composition of free-living (FL) and particle-attached (PA) bacterial groups in marine ecosystems, few studies have focused on the FL and PA bacterial communities in large and shallow eutrophic lakes. Furthermore, the assembly processes of the FL and PA bacterial communities have not been investigated. To illustrate the differences between PA (≥5.0 μm) and FL (0.22-5.0 μm) bacterial communities, samples were collected from 13 different sites in Taihu Lake, China. A higher diversity of the PA bacterial group than that of the FL group was observed, and significant differences in bacterial community composition between FL and PA groups were found (analysis of similarity, R = 0.2425, P < 0.001). Moreover, the two groups exhibited different relationships with environmental factors and geographic distance. Environmental factors played more important roles in affecting the FL bacterial community. A deterministic process was found as the primary factor driving the community of FL bacteria in Taihu Lake. However, the PA bacterial group was characterized by insignificant results of partial Mantel tests, which indicated that the community assembly was controlled by unknown processes.

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia.

Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.

Methanogenic Biocathode Microbial Community Development and the Role of Bacteria.

The cathode microbial community of a methanogenic bioelectrochemical system (BES) is key to the efficient conversion of carbon dioxide (CO2) to methane (CH4) with application to biogas upgrading. The objective of this study was to compare the performance and microbial community composition of a biocathode inoculated with a mixed methanogenic (MM) culture to a biocathode inoculated with an enriched hydrogenotrophic methanogenic (EHM) culture, developed from the MM culture following pre-enrichment with H2 and CO2 as the only externally supplied electron donor and carbon source, respectively. Using an adjacent Ag/AgCl reference electrode, biocathode potential was poised at -0.8 V (versus SHE) using a potentiostat, with the bioanode acting as the counter electrode. When normalized to cathode biofilm biomass, the methane production in the MM- and EHM-biocathode was 0.153 ± 0.010 and 0.586 ± 0.029 mmol CH4/mg biomass-day, respectively. This study showed that H2/CO2 pre-enriched inoculum enhanced biocathode CH4 production, although the archaeal communities in both biocathodes converged primarily (86-100%) on a phylotype closely related to Methanobrevibacter arboriphilus. The bacterial community of the MM-biocathode was similar to that of the MM inoculum but was enriched in Spirochaetes and other nonexoelectrogenic, fermentative Bacteria. In contrast, the EHM-biocathode bacterial community was enriched in Proteobacteria, exoelectrogens, and putative producers of electron shuttle mediators. Similar biomass levels were detected in the MM- and EHM-biocathodes. Thus, although the archaeal communities were similar in the two biocathodes, the difference in bacterial community composition was likely responsible for the 3.8-fold larger CH4 production rate observed in the EHM-biocathode. Roles for abundant OTUs identified in the biofilm and inoculum cultures were highlighted on the basis of previous reports.

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free‐living and particle‐attached assemblages

AbstractIn eutrophic lakes, heterotrophic bacteria are closely associated with algal detritus and play a crucial role in nutrient cycling. However, the seasonal and spatial dynamics of free‐living (FL) and particle‐attached (PA) bacteria and the environmental factors shaping this relationship remain poorly understood. To address this issue, we explored the spatiotemporal patterns of bacterial community composition (BCC) in Lake Taihu, China, using terminal restriction fragment length polymorphism (T‐RFLP) and 454‐tag pyrosequencing of 16S rRNA gene. We generated a total of 218,027 high quality non‐cyanobacterial sequence reads that resulted in 4940 OTUs (97% cutoff), with Actinobacteria, β‐ and α‐proteobacteria being the predominant taxa. Although PA communities contained significantly higher alpha‐diversity than FL ones, we found that 59% of OTUs, that accounted for 96% of the total reads, were shared by both communities. The high degree of overlap between FL and PA communities indicates a high rate of dispersal potential, highlighting an underestimated connectivity and potentially similar ecological role for these two components. Distinct seasonal trends were recorded in both FL and PA communities, while spatial differences in BCC were small. In addition, both FL and PA bacterial communities exhibited similar patterns and synchrony, correlated to water temperature, nitrate and total suspended solids (TSS). Accordingly, the effects of eutrophication and hydrodynamics on the phylogenetic overlap and diversity between FL and PA communities were discussed.

Bacterial Signatures of "Red-Operculum" Disease in the Gut of Crucian Carp (Carassius auratus).

Fish gut microbiota play important roles in fish immunity, nutrition, and the adaptation to environmental changes. To date, few studies have focused on the interactions among environmental factors, fish diseases, and gut microbiota compositions. We compared the gut bacterial communities of healthy crucian carps (Carassius auratus) with those of individuals affected by "red-operculum" disease and corresponding water and sediment microbiota in four fish farm ponds. Distinct gut bacterial communities were observed in healthy and diseased fish. The bacterial communities of diseased fish were less diverse and stable than those of healthy individuals. The differences in bacterial community compositions between diseased and healthy fish were explained by the changes in the relative abundances of some specific bacterial OTUs, which belonged to the genera such as Vibrio, Aeromonas, and Shewanella, and they were prevalent in diseased fish, but rare or even absent in environmental samples. Water temperature and ammonia concentration were the two most important environmental factors that impacted gut microbiota in diseased fish. These results highlighted the surge of some potential pathogens as bacterial signatures that were associated with "red-operculum" disease in crucian carps.

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas

Coral reefs are subject to coral bleaching manifested by the loss of endosymbiotic algae from coral host tissue. Besides algae, corals associate with bacteria. In particular, bacteria residing in the surface mucus layer are thought to mediate coral health, but their role in coral bleaching is unknown. We collected mucus from bleached and healthy Porites lobata colonies in the Persian/Arabian Gulf (PAG) and the Red Sea (RS) to investigate bacterial microbiome composition using 16S rRNA gene amplicon sequencing. We found that bacterial community structure was notably similar in bleached and healthy corals, and the most abundant bacterial taxa were identical. However, fine-scale differences in bacterial community composition between the PAG and RS were present and aligned with predicted differences in sulfur- and nitrogen-cycling processes. Based on our data, we argue that bleached corals benefit from the stable composition of mucus bacteria that resemble their healthy coral counterparts and presumably provide a conserved suite of protective functions, but monitoring of post-bleaching survival is needed to further confirm this assumption. Conversely, fine-scale site-specific differences highlight flexibility of the bacterial microbiome that may underlie adjustment to local environmental conditions and contribute to the widespread success of Porites lobata.

Bottle effects alter taxonomic composition of wetland soil bacterial communities during the denitrification enzyme activity assay

The denitrification enzyme activity assay (DEA) and other ex situ, incubation-based methods are widely used for measuring biogeochemical transformations. DEA does not provide direct measurements of denitrification rates in situ, but rather denitrification potential under laboratory conditions over the course of an incubation with resource limitations removed. Despite recognized limitations, DEA has several advantages. In particular, it is a relatively simple and low-cost method considered reliable for comparing relative differences in denitrification, for example between areas subjected to different management treatments. However, a critical but, to our knowledge, untested assumption of DEA is that bacterial composition remains static during the assay, i.e., the microbial community being assayed is equivalent to the original community collected from the field. If this assumption is violated, it could result in flawed estimates of relative differences between samples. We tested the static-community assumption using high-throughput sequencing to measure differences in bacterial community composition between samples from two different wetland vegetation types over the course of standard DEA incubations. We also compared samples that were or were not treated with a standard amendment solution to differentiate amendment effects from “bottle effects” of time spent under storage and laboratory conditions. We found that initially distinct bacterial communities became less similar to each other during short-term cold storage, but then became more similar during incubation, with a net result of samples converging in composition. Surprisingly, there were no effects of amendment solution; bottle effects alone accounted for these changes. This raises concern that potentially important differences in wetland denitrification, or other processes measured using ex situ methods, could be obscured by changes in bacterial community composition that arise as an artifact of laboratory incubations.

Exploring gastric bacterial community in young pigs.

Microbiota plays an important role in the homeostasis of the gastrointestinal tract. Understanding the variations of the commensal microbiota composition is crucial for a more efficient control of enteric infectious diseases and for the reduction of the use of antibiotics in animal production, which are the main points of interest for improved animal healthcare and welfare and for consumer health protection. Even though the intestinal microbiota has been extensively studied, little is known about the gastric microbiota. This pilot study was aimed at a descriptive analysis of the gastric microbiota in healthy pigs and at the identification of any differences among four potentially distinct microbial niches in the stomach. Gastric mucosal samples from the oxyntic area, the pylorus and the gastric groove, and a sample of gastric contents were collected from four healthy weaned pigs. Bacterial DNA was isolated and extracted from each sample and amplicons from the V6 region of the 16S rRNA gene were sequenced using Ion Torrent PGM. The data were analysed by an “unsupervised” and a “supervised” approach in the Ribosomal Database Project (RDP) pipeline. Proteobacteria was the dominant phylum in all the samples. Differences in bacterial community composition were found between mucosal and content samples (one-way ANOSIM pairwise post hoc test, p < 0.05); instead, the different mucosal regions did not show differences between them. The mucosal samples were characterised by Herbiconiux and Brevundimonas, two genera which include cellulolytic and xylanolytic strains. Nevertheless, additional larger trials are needed to support the data presented in this pilot study and to increase the knowledge regarding the resident microbiota of the stomach.