Environmental Bacterial Communities Research Articles

Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment

Historically, the environment has been viewed as a passive deposit of antimicrobial resistance mechanisms, where bacteria show biological cost for maintenance of these genes. Thus, in the absence of antimicrobial pressure, it is expected that they disappear from environmental bacterial communities. To test this scenario, we studied native IntI1 functionality of 11 class 1 integron-positive environmental strains of distant genera collected in cold and subtropical forests of Argentina. We found natural competence and successful site-specific insertion with no significant fitness cost of both aadB and blaVIM-2 antimicrobial resistance gene cassettes, in a model system without antibiotic pressure. A bidirectional flow of antimicrobial resistance gene cassettes between natural and nosocomial habitats is proposed, which implies an active role of the open environment as a reservoir, recipient and source of antimicrobial resistance mechanisms, outlining an environmental threat where novel concepts of rational use of antibiotics are extremely urgent and mandatory.

Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor

BackgroundDuckweed (family Lemnaceae) has recently been recognized as an ideal biomass feedstock for biofuel production due to its rapid growth and high starch content, which inspired interest in improving their productivity. Since microbes that co-exist with plants are known to have significant effects on their growth according to the previous studies for terrestrial plants, this study has attempted to understand the plant–microbial interactions of a duckweed, Lemna minor, focusing on the growth promotion/inhibition effects so as to assess the possibility of accelerated duckweed production by modifying co-existing bacterial community.ResultsCo-cultivation of aseptic L. minor and bacterial communities collected from various aquatic environments resulted in changes in duckweed growth ranging from −24 to +14% compared to aseptic control. A number of bacterial strains were isolated from both growth-promoting and growth-inhibitory communities, and examined for their co-existing effects on duckweed growth. Irrespective of the source, each strain showed promotive, inhibitory, or neutral effects when individually co-cultured with L. minor. To further analyze the interactions among these bacterial strains in a community, binary combinations of promotive and inhibitory strains were co-cultured with aseptic L. minor, resulting in that combinations of promotive–promotive or inhibitory–inhibitory strains generally showed effects similar to those of individual strains. However, combinations of promotive–inhibitory strains tended to show inhibitory effects while only Aquitalea magnusonii H3 exerted its plant growth-promoting effect in all combinations tested.ConclusionSignificant change in biomass production was observed when duckweed was co-cultivated with environmental bacterial communities. Promotive, neutral, and inhibitory bacteria in the community would synergistically determine the effects. The results indicate the possibility of improving duckweed biomass production via regulation of co-existing bacterial communities.

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments.

Community-level physiological profiling (CLPP) analyses from very diverse environments are frequently used with the aim of characterizing the metabolic versatility of whole environmental bacterial communities. While the limitations of the methodology for the characterization of whole communities are well known, we propose that CLPP combined with high-throughput sequencing and qPCR can be utilized to identify the copiotrophic, fast-growing fraction of the bacterial community of soil environments, where oligotrophic taxa are usually dominant. In the present work we have used this approach to analyze samples of litter and soil from a coniferous forest in the Czech Republic using BIOLOG GN2 plates. Monosaccharides and amino acids were utilized significantly faster than other C substrates, such as organic acids, in both litter and soil samples. Bacterial biodiversity in CLPP wells was significantly lower than in the original community, independently of the carbon source. Bacterial communities became highly enriched in taxa that typically showed low abundance in the original soil, belonging mostly to the Gammaproteobacteria and the genus Pseudomonas, indicating that the copiotrophic strains, favoured by the high nutrient content, are rare in forest litter and soil. In contrast, taxa abundant in the original samples were rarely found to grow at sufficient rates under the CLPP conditions. Our results show that CLPP is useful to detect copiotrophic bacteria from the soil environments and that bacterial growth is substrate specific.

Impact of environmental bacterial communities on fish health in marine recirculating aquaculture systems

Marine cultured fish diseases caused by bacteria in recirculating aquaculture systems (RASs) greatly threaten fish aquaculture. To date, the dynamics of bacterial populations in RAS and their impacts to fish health remain largely unknown. In the present study, the bacterial communities in the water from two different marine RASs were analyzed using pyrosequencing technique. Fish disease syndromes and mortality had been reported from one RAS (RAS-d) while the fish in the other RAS remained healthy (RAS-h). The diversity of bacteria in each RAS and the abundance of each bacterium were identified based on sequencing the V4 hypervariable region of the 16S rRNA gene. A total number of 107,476 effective sequences were obtained from the pyrosequencing results. 640 and 844 operational taxonomic units (OTUs) were identified in RAS-d and RAS-h, respectively. In order level, tags annotation showed that Vibrionales and Flavobacteriales were the predominant strains in RAS-d with a relative abundance 50.5% and 36.5%, respectively. In contrast, the bacterial community in RAS-h contained 35.8% Vibrionales, 17.3% Alteromonadales, 10.7% Rhodobacterales, 7.43% Kordiimonadales, and 6.26% Oceanospirillales. In addition, the Vibrionaceae in the RAS-d represented 6.98% of the population which was significantly higher than that in RAS-h (0.40%). More potential pathogenic bacteria in fish, such as Vibrio harveyi, Vibrio rotiferianus were also found in the bacterial population in RAS-d. The results also showed that the bacteria community in RAS-h was more diverse and balanced than in RAS-d. These findings of this study suggested a potential correlation between fish diseases and environmental bacterial populations.

Seasonal and spatial variations in diversity and abundance of bacterial laccase-like genes in sediments of a subtropical mangrove ecosystem

Laccases, involved in degradation of soil/sediment organic matter (SOM), play an important role in C and nutrient cycling in ecosystems. Laccases of fungal origins have been extensively studied, but only few reports are available for bacterial laccase-like genes, especially in coastal mangrove ecosystems. Therefore, we investigated the seasonal diversity and abundance of bacterial laccase-like genes in coastal mangrove sediments, and then compared to other ecosystems including Forest, Grassland, Fen and Bog. Additionally, the correlations between environmental factors and bacterial laccase-like communities were analyzed. The results demonstrated that the diversity and abundance of bacterial laccase-like genes in this mangrove ecosystem largely varied in sediment types and sampling seasons, and the microbial communities inferred by the functional genes included Proteobacteria, Actinobacteria, Bacteroidetes and some Unknown species as the major groups. In comparison, bacterial laccase-like communities in mangrove sediments were significantly different with the referenced ecosystems. The variations of total contents of C and N in soils/sediments are proposed to be the primary reasons for the differences of bacterial laccase-like genes among ecosystems. Moreover, the diversity index was negatively correlated with C:P and N:P, while the abundance showed a positive/negative correlation with water content and redox potential in this mangrove ecosystem, indicating a significant impact of other environmental factors, such as P and redox potential, on the diversity, distribution and the abundance of bacterial laccase-like genes which were underestimated in the previous research. Taking together, hereby P is proposed as a regulatory and limiting element for microbial SOM degradation through the laccases-initiated enzymatic reaction.

The biogeography of the atlantic salmon (Salmo salar) gut microbiome.

Although understood in many vertebrate systems, the natural diversity of host-associated microbiota has been little studied in teleosts. For migratory fishes, successful exploitation of multiple habitats may affect and be affected by the composition of the intestinal microbiome. We collected 96 Salmo salar from across the Atlantic encompassing both freshwater and marine phases. Dramatic differences between environmental and gut bacterial communities were observed. Furthermore, community composition was not significantly impacted by geography. Instead life-cycle stage strongly defined both the diversity and identity of microbial assemblages in the gut, with evidence for community destabilisation in migratory phases. Mycoplasmataceae phylotypes were abundantly recovered in all life-cycle stages. Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.

Comprehensive mapping of environmental microbiomes in terms of their compositional features remains a great challenge in understanding the microbial biosphere of the Earth. It bears promise to identify the driving forces behind the observed community patterns and whether community assembly happens deterministically. Advances in Next Generation Sequencing allow large community profiling studies, exceeding sequencing data output of conventional methods in scale by orders of magnitude. However, appropriate collection systems are still in a nascent state. We here present a database of 20,427 diverse environmental 16S rRNA profiles from 2,426 independent studies, which forms the foundation of our meta-analysis. We conducted a sample size adaptive all-against-all beta diversity comparison while also respecting phylogenetic relationships of Operational Taxonomic Units(OTUs). After conventional hierarchical clustering we systematically test for enrichment of Environmental Ontology terms and their abstractions in all possible clusters. This post-hoc algorithm provides a novel formalism that quantifies to what extend compositional and semantic similarity of microbial community samples coincide. We automatically visualize significantly enriched subclusters on a comprehensive dendrogram of microbial communities. As a result we obtain the hitherto most differentiated and comprehensive view on global patterns of microbial community diversity. We observe strong clusterability of microbial communities in ecosystems such as human/mammal-associated, geothermal, fresh water, plant-associated, soils and rhizosphere microbiomes, whereas hypersaline and anthropogenic samples are less homogeneous. Moreover, saline samples appear less cohesive in terms of compositional properties than previously reported.

Matrix-bound phosphine in the paddy soils of South China and its relationship to environmental factors and bacterial composition

Purpose Phosphine is a significant gaseous carrier in the P cycle. The matrix-bound phosphine in the paddy soils and its relationship to environmental variables and bacterial community composition were studied.

Environmental factors shaping the abundance and distribution of laccase-encoding bacterial community with potential phenolic oxidase capacity during composting.

Increasing molecular evidence points to a wide occurrence of laccase-like multicopper oxidase (LMCO)-encoding genes in bacteria. Most researches mainly focused on the bacterial LMCO diversity, whereas the processes and the environmental factors responsible for structuring bacterial LMCO communities remain relatively unknown in a composting system. Six gene libraries were constructed from samples in representative stages during composting. A total of 185 sequences obtained from sample DNA extracts were classified to 59 operational taxonomic units (OTUs) based on 10 % cutoff. The distribution profile of bacterial LMCO genes showed that proteobacterial- and actinobacterial-associated species were the dominant communities during composting. Pearson correlation analysis indicated that the pile temperature and water-soluble carbon (WSC) content were significantly positively correlated with bacterial LMCO gene OTU numbers, Chao1 and Shannon index, whereas the humic acid (HA)-like carbon content had the most significant effect on the distribution of the bacterial LMCO genes during composting by redundancy analysis. These findings will improve the understanding of the mutual relationship between environmental factors and bacterial LMCO community compositions in composting.

PH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing.

The Qiantang River is a typical freshwater ecosystem that acts as an irreplaceable water source in Zhejiang Province in southeastern China. However, the effects of environmental factors on the bacterial community of this freshwater ecosystem have not been determined. In this study, seven sediment samples were collected along the river. Their bacterial communities were identified using 454 high-throughput sequencing, and the primary environmental factors responsible for shaping the community structure were analyzed. The number of bacterial operational taxonomic units (OTUs) ranged from 2637 to 3933. Using a linear-regression analysis, the OTU numbers were significantly positively correlated with pH (r = 0.832, p < 0.05) and negatively correlated with nitrate concentration (r = −0.805, p < 0.05). A redundancy analysis (RDA) was also performed to test the relationship between the environmental factors and bacterial community composition. The results indicated that pH (p < 0.05) and nitrate concentration (p < 0.05) were the most significant factors that determined the community distribution of sediment bacteria.

Shifts in the metabolic function of a benthic estuarine microbial community following a single pulse exposure to silver nanoparticles

The increasing use of silver nanoparticles (AgNPs) as a biocidal agent and their potential accumulation in sediments may threaten non-target natural environmental bacterial communities. In this study a microcosm approach was established to investigate the effects of well characterized OECD AgNPs (NM-300) on the function of the bacterial community inhabiting marine estuarine sediments (salinity 31‰). The results showed that a single pulse of NM-300 AgNPs (1 mg L−1) that led to sediment concentrations below 6 mg Ag kg−1 dry weight inhibited the bacterial utilization of environmentally relevant carbon substrates. As a result, the functional diversity changed, but recovered after 120 h under the experimental conditions. This microcosm study suggests that AgNPs under environmentally relevant experimental conditions can negatively affect bacterial function and provides an insight into the understanding of the bacterial community response and resilience to AgNPs exposure, important for informing relevant regulatory measures.

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.

Spatial abundance and diversity of bacterioplankton in a typical stream-forming ecosystem, Huangqian Reservoir, China.

The specific freshwater environment of reservoirs formed by streams has not been well studied. In this paper, the bacterioplankton community in such a reservoir, the Huangqian Reservoir in eastern China, was described using culture-independent molecular methods. We found that the most dominant bacterioplankton were affiliated with Cyanobacteria, followed by Betaproteobacteria, Bacteroidetes, Gammaproteobacteria, and Actinobacteria. Both bacterial abundance and diversity increased along the direction of water flow, and the 16S rRNA gene copy number in the water outlet was nearly an order of magnitude higher than that in the water inlet. Pearson correlation analyses indicated that nitrate had a significantly negative correlation with the bacterial abundance (p < 0.05) and that ammonium was positively correlated with bacterial abundance (p < 0.05). Interestingly, owing to a remarkably negative correlation (p < 0.01), the ratio of nitrate and ammonium might serve as a good pre dictor of the relative abundance of bacterioplankton. According to redundancy analysis, nitrate and dissolved oxygen were the major factors influencing the bacterial communities. In addition, we attempted to determine the reasons why such a reservoir could maintain good ecological balance for a period of decades, and we found that the environmental factors and bacterial communities both played critical roles. This research will benefit our understanding of bacterial communities and their surrounding environments in freshwater ecosystems.

The Potential of Antibiotic Alternatives for Enriching Beneficial Microbiota in Litter

Alternative growth promoters such as probiotics, prebiotics and competitive exclusion products have been used with some success in animal production. A compelling application of these products is their potential to reduce pathogen populations by altering the environmental bacterial community of a built up litter system over multiple grow-outs. The objectives of this study were determine the bacterial composition of the litter over multiple production cycles and describe the impact of alternative growth promoters on composition and abundance of bacteria viewed as beneficial or pathogenic. In this study, probiotics were found to have the ability to positively alter the litter bacterial community. Bacterial diversity and the proportion of the community consisting of beneficial bacteria were increased in the litter when probiotics were administered. As the litter aged, diversity decreased and the composition shifted from Firmicute to Actinobacteria. Detection of pathogenic Clostridium species increased in litter with time regardless of the type of product used. However, detection of Enterococcus cecorum decreased over time and treatments produced less E. cecorum in reused litter after 1 flock cycle. These findings suggest that administering alternatives to antibiotics can change the litter bacterial composition, increase the abundance of beneficial bacteria and reduce the prevalence of some pathogens.

Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria

Culture-dependent methods for bacterial community analysis are currently considered obsolete; therefore, molecular techniques are usually used instead. The results of the current study on hydrocarbonoclastic bacteria in various oily habitats in Kuwait showed however, that the bacterial identities varied dramatically according to the analytical approach used. For six desert and six seawater samples used in this study, the culture-independent and culture-dependent techniques each led to a unique bacterial composition. Problems related to the culture-dependent technique are well known. The results of the current study highlighted bias problems other than those already recorded in the literature for the molecular approaches. Thus, for example, in contrast to the culture-dependent technique, the primers used in the molecular approach preferentially amplified the 16S rDNAs of hydrocarbonoclastic bacteria in total genomic DNAs of all the studied environmental samples, and in addition, failed to reveal in any environmental sample members of the Actinobacteria. The primers used in the molecular approach also amplified certain “pure” 16S rDNAs, but failed to do so when these DNAs were in mixture. In view of these results, it is recommended that the two analytical approaches should be used simultaneously because their combined results would reflect the bacterial community composition more precisely than either of them can do alone.

Correlations between Environmental Variables and Bacterial Community Structures Suggest Fe(III) and Vinyl Chloride Reduction As Antagonistic Terminal Electron-Accepting Processes

Natural attenuation of anaerobic aquifers contaminated with tetrachloroethene (PCE) often results in the accumulation of the intermediates cis-dichloroethene and vinyl chloride (VC) which are even more toxic than the parent compound. Reasons for this accumulation were investigated in a PCE-contaminated aquifer in which VC accumulation has previously been shown to occur using stable isotope techniques. Multifactorial analysis of bacterial community structure data and environmental variables showed that in general terminal electron-accepting processes were shaping the bacterial community structures. Both VC and Fe(III) reduction were key but antagonistic terminal electron-accepting processes. The phylogenetic affiliation of terminal restriction fragments (T-RFs), together with correlation analyses, showed that T-RFs having significant correlation with VC reduction were closely affiliated to the genus Dehalococcoides and to uncultured bacteria belonging to the "Lahn Cluster" within the class Dehalococcoidetes. A T-RF that negatively correlated with a "Lahn Cluster" T-RF was affiliated to the genus Rhodoferax that contains members identified as iron-reducing bacteria. The higher affinity of Fe(III)-reducing bacteria for hydrogen compared with VC-reducing bacteria might explain why VC accumulated locally at the studied site. In conclusion, the combination of molecular and numerical ecology approaches was helpful to identify reasons for the accumulation of toxic dechlorination intermediates and could become a useful tool for characterizing contaminated sites in general.

Risk assessment of oxytetracycline in water phase to major sediment bacterial community: A water-sediment microcosm study

With an increasing need for assessing the risk of aquaculture antibiotics, there has been growing interest in their fate and effect on sedimentary bacteria. Here we show the risk assessment for oxytetracycline (OTC) use in seawater and its subsequent transfer to sediment, and illustrate that the sediment bacterial community was stable against OTC at dosed concentrations. Water-sediment microcosm experiments were conducted to simulate quiescent aquaculture conditions. The sorption coefficient (Kd) was 12.3–44.2mL/g, which is lower than the previous reports employing vigorous mixing. In a denaturing gradient gel electrophoresis (DGGE) analysis, the addition of OTC at 50μg/L into the water phase had little effect on the major sediment bacterial community structure. This finding suggests that low concentrations of OTC in the water phase – such as those used within many aquaculture operations – do not pose a high risk of causing major changes in environmental sediment bacterial community structures.

Impact of treated wastewater irrigation on antibiotic resistance in the soil microbiome

The reuse of treated wastewater (TWW) for irrigation is a practical solution for overcoming water scarcity, especially in arid and semiarid regions of the world. However, there are several potential environmental and health-related risks associated with this practice. One such risk stems from the fact that TWW irrigation may increase antibiotic resistance (AR) levels in soil bacteria, potentially contributing to the global propagation of clinical AR. Wastewater treatment plant (WWTP) effluents have been recognized as significant environmental AR reservoirs due to selective pressure generated by antibiotics and other compounds that are frequently detected in effluents. This review summarizes a myriad of recent studies that have assessed the impact of anthropogenic practices on AR in environmental bacterial communities, with specific emphasis on elucidating the potential effects of TWW irrigation on AR in the soil microbiome. Based on the current state of the art, we conclude that contradictory to freshwater environments where WWTP effluent influx tends to expand antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes levels, TWW irrigation does not seem to impact AR levels in the soil microbiome. Although this conclusion is a cause for cautious optimism regarding the future implementation of TWW irrigation, we conclude that further studies aimed at assessing the scope of horizontal gene transfer between effluent-associated ARB and soil bacteria need to be further conducted before ruling out the possible contribution of TWW irrigation to antibiotic-resistant reservoirs in irrigated soils.

A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences

BackgroundBroad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail.ResultsIn this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature.ConclusionsThe method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D.armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca.55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.