Indigenous Microbial Communities Research Articles

Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes.

High-altitude Andean lakes (HAAL) are a treasure chest for microbiological research in South America. Their indigenous microbial communities are exposed to extremely high UV irradiation and to multiple chemical extremes (Arsenic, high salt content, alkalinity). Microbes are found both, free-living or associated into microbial mats with different degrees of mineralization and lithification, including unique modern stromatolites located at 3570 m above sea level. Characterization of these polyextremophilic microbes began only recently, employing morphological and phylogenetic methods as well as high-throughput sequencing and proteomics approach. Aside from providing a general overview on microbial communities, special attention is given to various survival strategies; HAAL's microbes present a complex system of shared genetic and physiological mechanisms (UV-resistome) based on UV photoreceptors and stress sensors with their corresponding response regulators, UV avoidance and protection strategies, damage tolerance and UV damage repair. Molecular information will be provided for what is, so far the most studied HAAL molecule, a CPD-Class I photolyase from Acinetobacter Ver3 (Laguna Verde, 4400 m). This work further proposes some strategies that make an appeal for the preservation of HAAL, a highly fragile environment that offers promising and ample research possibilities.

Development and Characterization of PCE-to-Ethene Dechlorinating Microcosms with Contaminated River Sediment.

An industrial complex in Wonju, contaminated with trichloroethene (TCE), was one of the most problematic sites in Korea. Despite repeated remedial trials for decades, chlorinated ethenes remained as sources of down-gradient groundwater contamination. Recent efforts were being made to remove the contaminants of the area, but knowledge of the indigenous microbial communities and their dechlorination abilities were unknown. Thus, the objectives of the present study were (i) to evaluate the dechlorination abilities of indigenous microbes at the contaminated site, (ii) to characterize which microbes and reductive dehalogenase genes were responsible for the dechlorination reactions, and (iii) to develop a PCE-to-ethene dechlorinating microbial consortium. An enrichment culture that dechlorinates PCE to ethene was obtained from Wonju stream, nearby a trichloroethene (TCE)-contaminated industrial complex. The community profiling revealed that known organohalide-respiring microbes, such as Geobacter, Desulfuromonas, and Dehalococcoides grew during the incubation with chlorinated ethenes. Although Chloroflexi populations (i.e., Longilinea and Bellilinea) were the most enriched in the sediment microcosms, those were not found in the transfer cultures. Based upon the results from pyrosequencing of 16S rRNA gene amplicons and qPCR using TaqMan chemistry, close relatives of Dehalococcoides mccartyi strains FL2 and GT seemed to be dominant and responsible for the complete detoxification of chlorinated ethenes in the transfer cultures. This study also demonstrated that the contaminated site harbors indigenous microbes that can convert PCE to ethene, and the developed consortium can be an important resource for future bioremediation efforts.

An experimental study on the inhibitory effect of high concentration bicarbonate on the reduction of U(VI) in groundwater by functionalized indigenous microbial communities

The anaerobic microcosms amended with 30 mM bicarbonate and without bicarbonate were established, respectively, and the reduction of U(VI) in the microcosms by functionalized indigenous microbial communities was investigated. Results of the chemical extraction and XANES analysis showed that the proportions of U(IV) in the microcosms amended with bicarbonate were 10 % lower than without bicarbonate at day 46. The amount of Cellulomonadaceae, Desulfovibrionaceae, Peptococcaceae and Veillonellaceae amended with bicarbonate was lower than without bicarbonate, so the reduction of U(VI) was less. The experimental results show that the high concentration bicarbonate has a significantly inhibitory effect on the reduction of U(VI).

An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.

Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

Of microbes and men.

In this issue of Diabetes Care , Simon et al. (1) report the results of a study testing the hypothesis that the administration of Lactobacillus reuteri in subjects without diabetes improves insulin sensitivity. A quick review of the background may help us put this work in context. Our digestive tract hosts some 2 kg of microbes, made up of ∼100 trillion microorganisms. Present in sparse colonies in the upper intestine, this indigenous microbial community (microbiota) jams into the cecum, colon, and rectum; the appendix is the ultimate shelter when antibiotics wage a mass killing. The taxonomy lists hundreds of species of bacteria (and minority groups of yeasts and viruses), whose collective genome is called microbiome (ninefold larger than our genome). Having coevolved with Homo sapiens , these microbes are so adapted to the human gut environment that they do not grow in culture as easily as do other germs and are therefore identified by their genetic material that is usually retrieved from feces. Microbiota have long been known to train our immune system, process indigestible foodstuffs, manufacture vitamins, and break down toxins and medications. In the past decade, variants of gut microbiome have been associated with diverse human diseases ranging from enterocolitis to psychiatric disorders. Of special interest to us is the association with obesity (2 …

Sorption and biodegradation characteristics of the selected pharmaceuticals and personal care products onto tropical soil.

In the present study, the sorption and biodegradation characteristics of five pharmaceutical and personal care products (PPCPs), including acetaminophen (ACT), carbamazepine (CBZ), crotamiton (CTMT), diethyltoluamide (DEET) and salicylic acid (SA), were studied in laboratory-batch experiments. Sorption kinetics experimental data showed that sorption systems under this study were more appropriately described by the pseudo second-order kinetics with a correlation coefficient (R2)>0.98. Sorption equilibrium data of almost all target compounds onto soil could be better described by the Freundlich sorption isotherm model. The adsorption results showed higher soil affinity for SA, following by ACT. Results also indicated a slight effect of pH on PPCP adsorption with lower pH causing lower adsorption of compounds onto the soil except for SA at pH 12. Moreover, adsorption of PPCPs onto the soil was influenced by natural organic matter (NOM) since the higher amount of NOM caused lower adsorption to the soil. Biodegradation studies of selected PPCPs by indigenous microbial community present in soil appeared that the removal rates of ACT, SA and DEET increased with time while no effect had been observed for the rest. This study suggests that the CBZ and CTMT can be considered as suitable chemical sewage indicators based on their low sorption affinity and high resistance to biodegradation.

Temporal and spatial variation of the human microbiota during pregnancy

Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 pregnant women, 15 of whom delivered preterm. From 40 of these women, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and weekly during gestation and monthly after delivery from the vagina, distal gut, saliva, and tooth/gum. Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions. Microbiota community taxonomic composition and diversity remained remarkably stable at all four body sites during pregnancy (P > 0.05 for trends over time). Prevalence of a Lactobacillus-poor vaginal community state type (CST 4) was inversely correlated with gestational age at delivery (P = 0.0039). Risk for preterm birth was more pronounced for subjects with CST 4 accompanied by elevated Gardnerella or Ureaplasma abundances. This finding was validated with a set of 246 vaginal specimens from nine women (four of whom delivered preterm). Most women experienced a postdelivery disturbance in the vaginal community characterized by a decrease in Lactobacillus species and an increase in diverse anaerobes such as Peptoniphilus, Prevotella, and Anaerococcus species. This disturbance was unrelated to gestational age at delivery and persisted for up to 1 y. These findings have important implications for predicting premature labor, a major global health problem, and for understanding the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.

Innovative biological approaches for monitoring and improving water quality.

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages.

Remediation of diesel‐contaminated soil using in situ chemical oxidation (ISCO) and the effects of common oxidants on the indigenous microbial community: a comparison study

AbstractBACKGROUNDIn this study, batch experiments were conducted using diesel‐contaminated soil collected from a former gas station to evaluate the efficiency of diesel removal by in situ chemical oxidation (ISCO) and the effects of different oxidants on the indigenous microbial community.RESULTSDiesel removal efficiencies by persulfate, permanganate, and hydrogen peroxide under different concentrations (1, 3, 5, and 10%) ranged from 48 to 93% during a 120‐day reaction. The performance of diesel removal in the oxidant‐alone systems was persulfate > permanganate > hydrogen peroxide. Oxidant persistence was positively correlated with diesel removal performance. Higher diesel removal efficiencies were observed in the chemical oxidation systems with the presence of microbes. The adverse effects of the oxidants on intrinsic microbes followed the sequence persulfate > permanganate ≈ hydrogen peroxide. The addition of hydrogen peroxide and permanganate caused increased microbial diversity while more serious destruction to the microbial community was observed in the persulfate solution due to low pH (<3.5).CONCLUSIONThe results suggest 1 to 3% of oxidant addition was more suitable for the application of ISCO coupled with intrinsic bioremediation. The addition of 5% oxidants could also be considered. However, pH should be controlled when persulfate is applied. © 2015 Society of Chemical Industry

Effect of fumigation with 1,3-dichloropropene on soil bacterial communities

1,3-Dichloropropene (1,3-D) is a potential candidate as a soil fumigant because of the restriction of methyl bromide (MB) in soil fumigation. So far, little is known about the bacteria diversity in 1,3-D fumigated soil. Therefore, the impact of 1,3-D on soil bacterial community was determined by the 16S rRNA gene amplicon 454 sequencing. A total of 230,617 valid reads and 19,366 OTUs were obtained from the thirteen samples. 454 sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Firmicutes were predominant phylum in soils. Bacterial diversity was affected initially, while recovered in the later treatments and soils from 1,3-D treatment plots had a higher bacterial diversity. The results of this study demonstrated that 1,3-D had only a short-term and transitory impact on the indigenous soil microbial community. Our study would provide useful information for evaluating ecological safety of 1,3-D in China.

Microbially induced corrosion of carbon steel in deep groundwater environment.

The metallic low and intermediate level radioactive waste generally consists of carbon steel and stainless steels. The corrosion rate of carbon steel in deep groundwater is typically low, unless the water is very acidic or microbial activity in the environment is high. Therefore, the assessment of microbially induced corrosion of carbon steel in deep bedrock environment has become important for evaluating the safety of disposal of radioactive waste. Here we studied the corrosion inducing ability of indigenous microbial community from a deep bedrock aquifer. Carbon steel coupons were exposed to anoxic groundwater from repository site 100 m depth (Olkiluoto, Finland) for periods of 3 and 8 months. The experiments were conducted at both in situ temperature and room temperature to investigate the response of microbial population to elevated temperature. Our results demonstrate that microorganisms from the deep bedrock aquifer benefit from carbon steel introduced to the nutrient poor anoxic deep groundwater environment. In the groundwater incubated with carbon steel the planktonic microbial community was more diverse and 100-fold more abundant compared to the environment without carbon steel. The betaproteobacteria were the most dominant bacterial class in all samples where carbon steel was present, whereas in groundwater incubated without carbon steel the microbial community had clearly less diversity. Microorganisms induced pitting corrosion and were found to cluster inside the corrosion pits. Temperature had an effect on the species composition of microbial community and also affected the corrosion deposits layer formed on the surface of carbon steel.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms.

Laboratory microcosm experiments were conducted to determine the decay kinetics of wastewater bacteria and the change of microbial communities in beach sand and seawater. Cultivation-based methods showed that common fecal indicator bacteria (FIBs; Escherichia coli, enterococci, and Clostridium perfringens) exhibited biphasic decay patterns in all microcosms. Enterococci and C. perfringens, but not E. coli, showed significantly smaller decay rates in beach sand than in seawater. Cultivation-independent qPCR quantification of 16S rRNA gene also showed significantly slower decrease of total bacterial densities in beach sand than in seawater. Microbial community analysis by next-generation sequencing (NGS) further illustrated that the decreasing relative abundance of wastewater bacteria was contrasted by the increase in indigenous beach sand and seawater microbiota, and the overall microbial community dynamics corresponded well with the decay of individual FIB populations. In summary, the differential decay of wastewater bacteria in beach sand and in seawater provides a kinetic explanation to the often-observed higher abundance of FIBs in beach sand, and the NGS-based microbial community analysis can provide valuable insights to understanding the fate of wastewater bacteria in the context of indigenous microbial communities in natural environments.

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation.

Successful bioremediation of oil pollution is based on a comprehensive understanding of the in situ physicochemical conditions and indigenous microbial communities as well as the interaction between microorganisms and geochemical variables. Nineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. Phylogenetic analysis indicated that the vast majority of sequences were related to the genera Arthrobacter, Dietzia, Pseudomonas, Rhodococcus, and Marinobacter, many of which contain known oil-degrading or oil-emulsifying species. Remarkably, a number of archaeal genera including Halalkalicoccus, Natronomonas, Haloterrigena, and Natrinema were found in relatively high abundance in some of the oil-contaminated soil samples, indicating that these Euryarchaeota may play an important ecological role in some oil-contaminated soils. This study offers a direct and reliable reference of the diversity of the microbial community in various oil-contaminated soils and may influence strategies for in situ bioremediation of oil pollution.

Biodiversity and degradation potential of oil-degrading bacteria isolated from deep-sea sediments of South Mid-Atlantic Ridge

The indigenous oil-degrading bacterial consortia MARA and MARB were enriched from the deep-sea sediments of South Mid-Atlantic Ridge (MAR) with crude oil as sole carbon and energy sources. Biodiversity and community analyses showed that members of α-Proteobacteria were the key players in consortium MARA, whereas those of γ-Proteobacteria were the key players in consortium MARB, which were studied by MiSeq sequencing method. Gravimetric method estimated the oil degradation rates of MARA and MARB to be 63.4% and 85.8%, respectively, after 20d. Eleven cultivable oil degraders with different morphologies were isolated. These strains were identified as Alcanivorax, Bacillus, Dietzia, Erythrobacter, Marinobacter, Nitratireductor, and Oceanicola based on 16S rRNA gene sequences. Three strains belonging to Dietzia exhibited the highest oil degradation capability. Results indicated that the intrinsic biodegradation capacity of oil contaminants by indigenous microbial communities exists in South MAR sediments.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

Laboratory simulation study of the solid-phase aerobic fermentation of nitrocellulose-containing wastewater sludge

The solid-phase aerobic degradation of nitrocellulose-containing sludge from the Aleksin Chemical Industrial Complex was studied by laboratory simulation with the use of activated indigenous microflora. This method applied to control physicochemical parameters (pH and aeration rate) led to an average nitrocellulose removal efficiency of about 26.3% during the first 9 days. The kinetic characteristics of the fermentation process were determined: the rate constants of nitrocellulose degradation varied from 0.026 to 0.036 day−1, and the half-life times were 20–27 days. Optimum operating conditions for nitrocellulose degradation by an indigenous microbial community were achieved at a sediment humidity level higher than 70%. Sodium humate was introduced into the test sludge as a rich source of organic materials in order to intensify the process of solid-state fermentation. Comparative analysis of the results revealed only an insignificant effect of physiological humate doses on nitrocellulose degradation. The maximum efficiency of nitrocellulose removal increased from 26.3% (base sample) to 29.4% upon the introduction of 1.6% sodium humate.

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany.

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.