Shifts In Bacterial Community Structure Research Articles

Standard inocula preparations reduce the bacterial diversity and reliability of regulatory biodegradation tests

OECD ready biodegradability tests have been central to understanding the biodegradation of chemicals from a regulatory perspective for many decades. They are not fit for contemporary prioritisation of chemicals based on persistence, however, due to the low concentration of inocula used, short duration and high variability between tests. Two OECD standard inoculum pretreatment methods (settlement and filtration) were investigated to observe their effect on the probability of biodegradation and associated changes in bacterial community structure and diversity of inocula sourced from the activated sludge process of wastewater treatment plants. Both settlement and filtration were shown to dramatically and significantly reduce the probability and increase the variability of biodegradation of 4-nitrophenol compared to the use of unprocessed inocula. These differences were associated with a significant hundred-fold reduction in cell numbers and solids content and a significant shift in bacterial community structure that was sometimes accompanied by significant reductions in detectable operational taxonomic unit richness and evenness. The natural variation (between different environments) and variation due to differential selection of bacterial communities (by different pretreatment methods) is offered as an explanation for the historical high variability in standard OECD ready biodegradability tests.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-013-2064-4) contains supplementary material, which is available to authorized users.

Differences in peptide decomposition rates and pathways between hypoxic and oxic coastal environments

Understanding the mechanisms of organic matter decomposition in hypoxic waters becomes more important globally with increasing hypoxia in coastal regions. Peptide decomposition rates were measured in low-oxygen bottom water and compared to those in oxygenated surface water of a stratified 18-m water column at a hypoxic northern Gulf of Mexico station. Water from each depth was spiked with small peptides alanine–valine–phenylalanine–alanine (AVFA) and VFA and incubated onboard for ca. 80h to determine peptide decomposition rates, decomposition products, and bacterial community structure shifts. Decomposition rates of amended peptides were twice as high in the bottom water as in the surface water, and the pathways of peptide decomposition differed. In surface waters, the small peptides were hydrolyzed into individual amino acids extracellularly by aminopeptidase, based on the analysis of hydrolyzed fragments; hydrolysis rates remained constant throughout the incubation period. In contrast, in bottom waters the amended peptides were metabolized rapidly into ammonium by bacteria through either direct uptake or tight coupling of extracellular hydrolysis and subsequent uptake after an initial adaptation period (~22h). Dissolved oxygen level did not affect peptide decomposition patterns significantly in surface or bottom water, when it was manipulated by sparging with air or nitrogen gas. The high efficiency of peptide decomposition in bottom waters corresponded to the rapid growth of several genera of Alpha- and Gammaproteobacteria. These bacterial species may have caused rapid peptide decomposition, but the exact mechanisms remain unclear. The high efficiency of peptide decomposition in hypoxic regions illustrates biogeochemical feedback to hypoxia formation in stratified coastal regions.

Spatial and temporal changes of bacterial communities inhabiting the well waters of Harkány spa

In this study, changes in the bacterial community composition of the well waters of Harkány Spa were examined. Physical and chemical properties of mixing subsurface cold and thermal karst waters were correlated to shifts in bacterial community structures analyzed by denaturing gradient gel electrophoresis (DGGE) and principal component analysis (PCA). In addition, mineral components of the pellets were investigated by scanning electron microscopy. Samples from the effluent waters of Büdöstapolca I and II, Matty and Thermal VI wells were taken seasonally in 2007 and 2008. The comparison of the results of DGGE and PCA analyses showed that bacterial communities from the Büdöstapolca wells were distinct from those of Matty and Thermal VI, but seasonal changes were not detected. According to the phylogenetic analysis of the excised DGGE bands, presence of chemolithotrophic Proteobacteria (Thiobacillus, Thiothrix, and distant relatives of Sulfurospirillum) were typical in the Büdöstapolca wells, while members of Actinobacteria (Plantibacter, Actinobacterium, Microbacterium) and Firmicutes (Planococcus) were characteristic to the Matty and Thermal VI wells. In the pellets pyrite framboid crystals were observed by electron microscopy, which are minerals known to be biologically induced by dissimilatory iron- and sulfur (sulfate)-reducing bacteria.

Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm

Insects are constantly adapting to human-driven landscape changes; however, the roles of their gut microbiota in these processes remain largely unknown. The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) (Coleoptera: Chrysomelidae) is a major corn pest that has been controlled via annual rotation between corn (Zea mays) and nonhost soybean (Glycine max) in the United States. This practice selected for a "rotation-resistant" variant (RR-WCR) with reduced ovipositional fidelity to cornfields. When in soybean fields, RR-WCRs also exhibit an elevated tolerance of antiherbivory defenses (i.e., cysteine protease inhibitors) expressed in soybean foliage. Here we show that gut bacterial microbiota is an important factor facilitating this corn specialist's (WCR's) physiological adaptation to brief soybean herbivory. Comparisons of gut microbiota between RR- and wild-type WCR (WT-WCR) revealed concomitant shifts in bacterial community structure with host adaptation to soybean diets. Antibiotic suppression of gut bacteria significantly reduced RR-WCR tolerance of soybean herbivory to the level of WT-WCR, whereas WT-WCR were unaffected. Our findings demonstrate that gut bacteria help to facilitate rapid adaptation of insects in managed ecosystems.

Bioaugmentation accelerates the shift of bacterial community structure against shock load: a case study of coking wastewater treatment by zeolite-sequencing batch reactor

Bioaugmentation with degrading bacteria is an effective method to improve the treatment of refractory industrial wastewater; nevertheless there were controversial opinions about the fate of inoculated bacteria and microbial community dynamics. In this study, two lab-scale sequencing batch reactors filled with modified zeolite were used to treat a coking wastewater with pyridine and quinoline shock load, and a bacterial consortium containing three degrading strains was added in one reactor for bioaugmentation. During 120-day operation, the bioaugmented reactor removed over 99 % pyridine, 99 % quinoline, 85 % TOC, 65 % COD, and 95 % NO₃⁻--N with higher resistance to the shock load than the non-bioaugmented reactor. Based on the terminal restriction fragment length polymorphism of 16S rDNA, bacterial community diversity increased in the bioaugmented reactor. Principal component analysis revealed that, to cope with the shock load, the indigenous bacterial community recovered to the initial structure by acclimatizing itself constantly to the inhospitable environment; but bioaugmentation accelerated the shift of whole bacterial community, resulting in a far different structure from the initial one. Canonical correspondence analysis indicated that the environmental parameters of pyridine, quinoline, TOC, and NO₃⁻--N had close negative correlations with bioaugmentation; and NH₃--N and COD were the main parameters to impact on the bacterial community changes and treatment efficiency.

Exceptional preservation of microbial lipids in Paleozoic to Mesoproterozoic sediments

Exceptional preservation of microbial lipids in Paleozoic to Mesoproterozoic sediments

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.

Soil Type Modestly Impacts Bacterial Community Succession Associated with Decomposing Grass Detrituspheres

Decomposition of plant residues has been widely studied; however, there is a lack of information on the dynamics of residue‐associated microbial taxa during decomposition and how it is affected by soil and residue types. It was hypothesized that distinct microbial communities from different soils would result in colonization of residues by different bacterial taxa and that there would be a shift in bacterial community structure during substrate degradation. A 2 × 2 factorial experiment with three replications was conducted consisting of Switchgrass (Panicum virgatum L.) and Rice (Oryza sativa L.) straw; two soil types (Sharkey and Marietta series); and four incubation periods (3, 23, 48, and 110 d; 25°C). Clone libraries were constructed from the unamended soils, pre‐incubation residues, and detritusphere (residues and adhering soil). Non‐metric multidimensional scaling of the detritusphere communities showed a large shift in the structure of the residue‐associated community following 3 d of decomposition. This shift coincided with disappearance of soluble C. Labile C availability appeared to be important for driving bacterial community succession during early colonization. At later stages of decomposition (Days 23–110), bacterial communities were less dynamic; however, there was partial segregation into two groups according to soil type. The relative abundance of Acidobacteria and Beta‐Proteobacteria were primarily responsible for community differences between the detrituspheres of the two soils. No effect on bacterial community dynamics and diversity due to residue type was observed. More striking was the relative similarity in bacterial types found to dominate the detrituspheres and point to the possibility that key functional community members are found widely in nature and that despite the huge diversity of soil bacteria, and some variation based on soil, a few dominant and widespread members came to the forefront during residue decomposition.

Depuration of Tetrodotoxin and Changes in Bacterial Communities in Pleurobranchea maculata Adults and Egg Masses Maintained in Captivity

Depuration of tetrodotoxin (TTX) was investigated in adult grey side-gilled sea slugs, Pleurobranchaea maculata, maintained in captivity on a TTX-free diet. Three adults were harvested every 21 days for 126 days, and TTX concentrations were measured in organs/tissues and egg masses. Automated rRNA intergenic spacer analysis (ARISA) was used to investigate bacterial community structure in selected samples. Linear modeling of adult data demonstrated a decline (P<0.001) in average total TTX concentrations over time. Temporal data obtained from a wild population showed similar depuration rates, indicating that once adults reach a certain size, or sexual maturity, TTX is no longer produced or acquired substantially. Depuration rates differed among organs, with concentrations in the heart declining the fastest. The gonads had the slowest and least significant depuration rate indicating, at most, weak depuration of this tissue. There was a strong correlation (R(2)=0.66) between TTX concentrations in the first-laid egg masses and total TTX in the corresponding adult. These data suggest that adult P. maculata transfer TTX to their offspring, and presumably that functions as a chemical defense. ARISA data showed a shift in bacterial community structure within 3 weeks of introduction to captivity. Based on the combined data, the exact origin of TTX in P. maculata is unclear, with evidence both in favor and against a dietary source, and endogenous or bacterial production.

Bacterial Consortium of Millepora dichotoma Exhibiting Unusual Multifocal Lesion Event in the Gulf of Eilat, Red Sea

Colonies of the hydrocoral Millepora dichotoma along the Gulf of Eilat are exhibiting unusual tissue lesions in the form of white spots. The emergence and rapid establishment of these multifocal tissue lesions was the first of its kind reported in this region. A characterization of this morphological anomaly revealed bleached tissues with a significant presence of bacteria in the tissue lesion area. To ascertain possible differences in microbial biota between the lesion area and non-affected tissues, we characterized the bacterial diversity in the two areas of these hydrocorals. Both culture-independent (molecular) and culture-dependent assays showed a shift in bacterial community structure between the healthy and affected tissues. Several 16S rRNA gene sequences retrieved from the affected tissues matched sequences of bacterial clones belonging to Alphaproteobacteria and Bacteroidetes members previously associated with various diseases in scleractinian corals.

Inhibition of fermentative hydrogen production by lignocellulose-derived compounds in mixed cultures

Dark fermentation using mixed cultures is an attractive biological process for producing hydrogen (H2) from lignocellulosic biomass at a low cost. Physicochemical pretreatment is generally used to convert lignocellulosic materials into monosaccharides. However, the processes also involved release degradation byproducts which can, in turn, inhibit microbial growth and metabolism and, hence, impact substrate conversion. In this study, the impact on H2 production of lignocellulose-derived compounds (i.e. furan derivatives, phenolic compounds and lignins) was assessed along with their effect on bacterial communities and metabolisms. Batch tests were carried out using xylose as model substrate (1.67molH2molxylose−1 in the control test). All the putative inhibitory compounds showed a significant negative impact on H2 production performance (ranging from 0.34 to 1.39molH2molxylose−1). The H2 yields were impacted more strongly by furan derivatives (0.40–0.51molH2molxylose−1) than by phenolic compounds (1.28–1.39molH2molxylose−1). Except for the batch tests supplemented with lignins, the lag phase was shorter for inhibitors having the highest molecular weight (8 days versus 22 days for the lowest MW). Variability of the lag phase was clearly related to a shift in bacterial community structure, as shown by multivariate ordination statistics. The decrease in H2 yield was associated with a decrease in the relative abundance of several H2-producing clostridial species. Interestingly, Clostridium beijerinkii was found to be more resistant to the inhibitors, making this bacterium an ideal candidate for H2 production from hydrolyzates of lignocellulosic biomass.

The temporal dynamics of bacterial communities across human anterior nares

The anterior nares (nostrils), are an important niche for bacterial colonization by both commensals and opportunistic pathogens. Here the temporal dynamics and variation of the global nasal bacterial community across 25 healthy volunteers was evaluated over 15 months. Overall, there was a global seasonal shift in bacterial community structure. Such a temporal shift was also strongly evident in the abundances of species such as Propionibacterium acnes and Staphylococcus epidermidis. However, such species dynamics over time was also inter-individual-dependent, and both individuals with highly stable communities and those with highly flexible communities could be defined. Even though the bacterial community of individual volunteers was thus generally variable over time and permanent carriage of a given species was seldomly observed, various species previously defined as constituting the core bacterial community could be identified as persistent in a subset of the volunteers suggesting that these same species also constitute to a 'temporal' core community.

Surface Water Linkages Regulate Trophic Interactions in a Groundwater Food Web

Groundwaters are increasingly viewed as resource-limited ecosystems in which fluxes of dissolved organic carbon (DOC) from surface water are efficiently mineralized by a consortium of microorganisms which are grazed by invertebrates. We tested for the effect of groundwater recharge on resource supply and trophic interactions by measuring physico-chemistry, microbial activity and biomass, structure of bacterial communities and invertebrate density at three sites intensively recharged with surface water. Comparison of measurements made in recharge and control well clusters at each site showed that groundwater recharge significantly increased fluxes of DOC and phosphate, elevated groundwater temperature, and diminished dissolved oxygen (DO). Microbial biomass and activity were significantly higher in recharge well clusters but stimulation of autochthonous microorganisms was not associated with a major shift in bacterial community structure. Invertebrate assemblages were not significantly more abundant in recharge well clusters and did not show any relationship with microbial biomass and activity. Microbial communities were bottom-up regulated by DOC and nutrient fluxes but trophic interactions between microorganisms and invertebrates were apparently limited by environmental stresses, particularly DO depletion and groundwater warming. Hydrological connectivity is a key factor regulating the function of DOC-based groundwater food webs as it influences both resource availability for microorganisms and environmental stresses which affect energy transfer to invertebrates and top-down control on microorganisms.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role.

Amplified ribosomal DNA restriction analysis as a routine tool to assess toxicant driven changes in hindgut bacterial populations of Porcellio dilatatus (Crustacea: Isopoda)

Changes in saprophytic organism's gut microbial communities may present a threat to organic matter breakdown which can ultimately lead to soil function impairment. In this study, Amplified Ribosomal DNA Restriction Analysis (ARDRA) was evaluated as a potential simple molecular tool to assess shifts in bacterial community structure in hindgut populations of Porcellio dilatatus exposed to contaminated food. This prospective tool can also be used for a variety of purposes and samples prior to the use of more specific and sophisticated methods.

Experimentally Simulated Global Warming and Nitrogen Enrichment Effects on Microbial Litter Decomposers in a Marsh

Atmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.

The Effect of a Sublethal Temperature Elevation on the Structure of Bacterial Communities Associated with the CoralPorites compressa

Evidence points to a link between environmental stressors, coral-associated bacteria, and coral disease; however, few studies have examined the details of this relationship under tightly controlled experimental conditions. To address this gap, an array of closed-system, precision-controlled experimental aquaria were used to investigate the effects of an abrupt 1°C above summer ambient temperature increase on the bacterial community structure and photophysiology ofPorites compressacorals. While the temperature treatment rapidly impacted the photophysiology of the coral host, it did not elicit a statistically significant shift in bacterial community structure from control, untreated corals as determined by terminal restriction fragment length polymorphism analysis of 16S rRNA genes. Two of three coral colonies harbored more closely related bacterial communities at the time of collection and, despite statistically significant shifts in bacterial community structure for both control and treatment corals during the 10-day acclimation period, maintained this relationship over the course of the experiment. The experimental design used in this study proved to be a robust, reproducible system for investigating coral microbiology in an aquarium setting.

Soil microbial community responses to the fungal endophyte Neotyphodium in Italian ryegrass

Cool-season grasses commonly harbor fungal endophytes in their aerial tissues. However the effects of these symbionts on soil microbial communities have rarely been investigated. Our objective was to explore microbial community responses in soils conditioned by plants of the annual grass Lolium multiflorum with contrasting levels of infection with the endophyte Neotyphodium occultans. At the end of the host growing season, we estimated the functional capacity of soil microbial communities (via catabolic response profiles), the contribution of fungi and bacteria to soil activity (via selective inhibition with antibiotics), and the structure of both microbial communities by molecular analyses. Soil conditioning by highly infected plants affected soil catabolic profiles and tended to increase soil fungal activity. We detected a shift in bacterial community structure while no changes were observed for fungi. Soil responses became evident even without changes in host plant biomass or soil organic carbon or total nitrogen content, suggesting that the endophyte modified host rhizodepositions during the conditioning phase. Our results have implications for the understanding of the reciprocal interactions between above and belowground communities, suggesting that plant-soil feedbacks can be mediated by this symbiosis.

Electricity generation from mixed volatile fatty acids using microbial fuel cells

Fermentative hydrogen production, as a process for clean energy recovery from organic wastewater, is limited by its low hydrogen yield due to incomplete conversion of substrates, with most of the fermentation products being volatile fatty acids (VFAs). Thus, further recovery of the energy from VFAs is expected. In this work, microbial fuel cell (MFC) was applied to recover energy in the form of electricity from mixed VFAs of acetate, propionate, and butyrate. Response surface methodology was adopted to investigate the relative contribution and possible interactions of the three components of VFAs. A stable electricity generation was demonstrated in MFCs after the enrichment of electrochemically active bacteria. Analysis showed that power density was more sensitive to the composition of mixed VFAs than coulombic efficiency. The electricity generation could mainly be attributed to the portion of acetate and propionate. However, the two components showed an antagonistic effect when propionate exceeded 19%, causing a decrease in coulombic efficiency. Butyrate was found to exert a negative impact on both power density and coulombic efficiency. Denaturing gradient gel electrophoresis profiles revealed the enrichment of electrochemically active bacteria from the inoculum sludge. Proteobacteria (Beta-, Delta-) and Bacteroidetes were predominant in all VFA-fed MFCs. Shifts in bacterial community structures were observed when different compositions of VFA mixtures were used as the electron donor. The overall electron recovery efficiency may be increased from 15.7% to 27.4% if fermentative hydrogen production and MFC processes are integrated.

Chemical and microbial properties in a greenhouse loamy soil after steam disinfestation alone or combined with CaO addition

Steam disinfestation represents an increasingly attractive strategy to control soil-borne pathogens and weeds both in greenhouses and field crops. Beyond pest control, steam injection has the potential to alter soil nutrient dynamics and composition of bacterial communities. This study investigated the impact of a soil-steaming method (the Bioflash™ system) on main chemical (total organic C, TOC; total N, TN; cation exchange capacity, CEC; exchangeable Na, K, Mg and Ca; KCl-extractable ammonium and nitrate, DTPA-exchangeable Mn) and microbial (microbial biomass C, MBC; genetic structure of bacterial communities) properties in a greenhouse loamy soil. Treatments were carried out by using a self-propelled soil-steaming machine operating at two steaming modes (deep or shallow) in combination or not with addition of an exothermically reacting compound (CaO at a 1000 kg ha −1 rate). Soils from a five-treatment (NS, non-steamed soil, DS, deep steam injection; DS + E, deep steam injection plus CaO; SS, shallow steam injection; SS + E, shallow steam injection plus CaO) plot block were sampled before steaming and after 8, 19, 54 and 91 days. Compositional shifts in the structure of soil bacterial communities were monitored by denaturing gradient gel electrophoresis (DGGE) fingerprinting of soil-extracted 16S rRNA gene fragments, using primers specific for Bacteria and Actinobacteria. Maximum soil temperature reached 70 °C (DS) and 82 °C (DS + E) in the 10–20 cm layer; and 50 °C (SS) and 53 °C (SS + E) in the 0–10 cm layer. TOC, TN, CEC, exchangeable Na, Mg and Ca were not statistically affected by soil steaming, CaO addition, depth of injection or their interactions. Conversely, SS promoted a large release of exchangeable K, notwithstanding CaO addition. Steam disinfestation significantly stimulated ammonium release, which further increased in CaO-treated steamed soils. Generally ammonium and nitrate pools varied oppositely, being the latter markedly reduced at the end of the observation period. Available Mn was significantly increased by soil steaming, but it was depressed when steaming was combined with CaO addition. Soil steaming markedly reduced the MBC, especially in DS-treated and SS-treated plots. The genetic structure of soil bacterial and actinobacterial communities was largely unresponsive to the steaming treatments. Even though the Bioflash™ system did not cause bacterial eradication or compositional shifts in bacterial community structure, soil steaming stimulated an increased release of soluble nutrients (K +, Mn 2+, NH 4 +–N). Over a longer perspective, excessive soil resources exploitation and potential risks of Mn toxicity should be cautiously considered especially in repeatedly (and eventually acid) steamed soils.