Dissimilatory iron and sulfate reduction by native microbial communities using lactate and citrate as carbon sources and electron donors

2019 ◽  
Vol 174 ◽  
pp. 524-531 ◽  
Author(s):  
Di Xia ◽  
Xiaoyun Yi ◽  
Yang Lu ◽  
Weilin Huang ◽  
Yingying Xie ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sulfate Reduction ◽  
Carbon Sources ◽  
Electron Donors

scholarly journals Dynamic Changes of Microbiome with the Utilization of Volatile Fatty Acids as Electron Donors for Denitrification

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1556
Author(s):  
Okkyoung Choi ◽  
Se-jin Cha ◽  
Hyunjin Kim ◽  
Hyunook Kim ◽  
Byoung-In Sang
Keyword(s):  
Fatty Acids ◽  
Microbial Community ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Carbon Sources ◽  
Electron Donors ◽  
Environmental Condition ◽  
Dynamic Changes ◽  
Nitrification And Denitrification ◽  
By Products

Volatile fatty acids can be used as carbon sources for denitrification and are easily supplied as by-products from the anaerobic digestion of waste materials. Nitrification and denitrification processes were carried out in a single reactor feeding volatile fatty acids as electron donors and the changes in microbial communities in the reactor were investigated. The microbial communities in the alternating aerobic and anoxic systems were different, and their structure flexibly changed within one reactor. Bacteroidetes and Firmicutes were highly distributed during denitrification, whereas Proteobacteria was a major phylum during nitrification. In addition, in the denitrification system, the microbial community was substrate dependent. It showed the sequential nitrogen removal in one reactor and the microbial community also followed the change of environmental condition, cyclic nitrification, and denitrification.

scholarly journals Mineral formation during bacterial sulfate reduction in the presence of different electron donors and carbon sources

2016 ◽  
Vol 435 ◽  
pp. 49-59 ◽  
Author(s):  
Xiqiu Han ◽  
Logan Schultz ◽  
Weiyan Zhang ◽  
Jihao Zhu ◽  
Fanxu Meng ◽  
...  
Keyword(s):  
Sulfate Reduction ◽  
Carbon Sources ◽  
Electron Donors ◽  
Bacterial Sulfate Reduction ◽  
Mineral Formation

scholarly journals Biotic and Abiotic Biostimulation for the Reduction of Hexavalent Chromium in Contaminated Aquifers

Water ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 89
Author(s):  
Andriani Galani ◽  
Daniel Mamais ◽  
Constantinos Noutsopoulos ◽  
Petra Anastopoulou ◽  
Alexia Varouxaki
Keyword(s):  
Microbial Communities ◽  
Hexavalent Chromium ◽  
Soil Column ◽  
Carbon Sources ◽  
Anaerobic Respiration ◽  
Electron Donors ◽  
Natural Soil ◽  
Contaminated Aquifer ◽  
Reducing Bacteria

Hexavalent chromium is a carcinogenic heavy metal that needs to be removed effectively from polluted aquifers in order to protect public health and the environment. This work aims to evaluate the reduction of Cr(VI) to Cr(III) in a contaminated aquifer through the stimulation of indigenous microbial communities with the addition of reductive agents. Soil-column experiments were conducted in the absence of oxygen and at hexavalent chromium (Cr(VI)) groundwater concentrations in the 1000–2000 μg/L range. Two carbon sources (molasses and EVO) and one iron electron donor (FeSO4·7H2O) were used as ways to stimulate the metabolism and proliferation of Cr(VI) reducing bacteria in-situ. The obtained results indicate that microbial anaerobic respiration and electron transfer can be fundamental to alleviate polluted groundwater from hazardous Cr(VI). The addition of organic electron donors increased significantly Cr(VI) reduction rates in comparison to natural soil attenuation rates. Furthermore, a combination of organic carbon and iron electron donors led to a longer life span of the remediation process and thus increased total Cr(VI) removal. This is the first study to investigate biotic and abiotic Cr(VI) removal by conducting experiments with natural soil and by applying biostimulation to modify the natural existing microbial communities.

scholarly journals Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Andrew Oliver ◽  
Brandon LaMere ◽  
Claudia Weihe ◽  
Stephen Wandro ◽  
Karen L. Lindsay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Reproductive Health ◽  
Microbial Communities ◽  
Carbon Sources ◽  
Amplicon Sequencing ◽  
Vaginal Microbiome ◽  
Content Type ◽  
Healthy Women ◽  
Healthy Pregnancy ◽  
Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

scholarly journals A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

2018 ◽  
Author(s):  
Manuel Kleiner ◽  
Xiaoli Dong ◽  
Tjorven Hinzke ◽  
Juliane Wippler ◽  
Erin Thorson ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Carbon Isotope ◽  
Isotope Ratio ◽  
Single Cells ◽  
Stable Carbon Isotope ◽  
Carbon Sources ◽  
Food Sources ◽  
Individual Species ◽  
Stable Carbon

AbstractMeasurements of the carbon stable isotope ratio (δ13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells.Here we present “direct Protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we show that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis showed that direct Protein-SIF confirms previous physiological hypotheses and can provide unexpected new insights into the symbionts’ metabolism. This confirms the usefulness of this new approach to accurately determine δ13C values for different species in microbial community samples.SignificanceTo understand the roles that microorganisms play in diverse environments such as the open ocean and the human intestinal tract, we need an understanding of their metabolism and physiology. A variety of methods such as metagenomics and metaproteomics exist to assess the metabolism of environmental microorganisms based on gene content and gene expression. These methods often only provide indirect evidence for which substrates are used by a microorganism in a community. The direct Protein-SIF method that we developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature. Direct Protein-SIF also allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.

scholarly journals Assessing the Microbial Communities in Four Different Daqusby Using PCR-DGGE, PLFA, and Biolog Analyses

2020 ◽  
Vol 69 (1) ◽  
pp. 27-37
Author(s):  
YUXI LING ◽  
WENYING LI ◽  
TONG TONG ◽  
ZUMING LI ◽  
QIAN LI ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Bacterial Biomass ◽  
Biolog Ecoplates ◽  
Different Types ◽  
Gradient Gel Electrophoresis ◽  
Plfa Analysis

Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

scholarly journals Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Electron Donors ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Metabolic Versatility ◽  
Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

Phosphate removal and sulfate reduction in a denitrification reactor packed with iron and wood as electron donors

2008 ◽  
Vol 58 (7) ◽  
pp. 1405-1413 ◽  
Author(s):  
Takahiro Yamashita ◽  
Ryoko Yamamoto-Ikemoto
Keyword(s):  
Sulfate Reduction ◽  
Phosphorus Removal ◽  
Iron Oxidation ◽  
Sulfur Oxidation ◽  
Phosphate Removal ◽  
Electron Donors ◽  
Rrna Gene ◽  
Phylogenetic Groups ◽  
Primer Sets ◽  
Heterotrophic Denitrification

Phosphorus removal and denitrification using iron and wood as electron donors were examined in a laboratory-scale biological filter reactor. Phosphorus removal and denitrification using iron and wood continued for 1,200 days of operation. Wood degradation by heterotrophic denitrification and iron oxidation by hydrogenotrophic denitrification occurred simultaneously. In the biofilm inside the wood, not only heterotrophic denitrification activity but also sulfate reduction and sulfur denitrification activities were recognized inside the wood, indicating that a sulfur oxidation-reduction cycle was established. Sulfate reduction and denitrification were accelerated with the addition of cellulose. Microbial communities of sulfate-reducing bacteria by PCR primer sets could be amplified in the biofilm in the reactors. The dissimilatory sulfite reductase gene and the 16S rRNA gene of six phylogenetic groups of SRB in the reactors were analyzed. Some SRB group-specific primers-amplification products were obtained inside the wood and around iron.

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