scholarly journals Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

2012 ◽  
Vol 78 (23) ◽  
pp. 8321-8330 ◽  
Author(s):  
Nicholas B. Justice ◽  
Chongle Pan ◽  
Ryan Mueller ◽  
Susan E. Spaulding ◽  
Vega Shah ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mine Drainage ◽  
Low Ph ◽  
Bacterial Cells ◽  
Content Type ◽  
Bacterial Proteins ◽  
Microbial Biofilms ◽  
Solution Interface ◽  
Mine Acid

ABSTRACTArchaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition fromBacteria- toArchaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the classThermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescentin situhybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment ofFerroplasmaand Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.

scholarly journals Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Christen L. Grettenberger ◽  
Alexandra R. Pearce ◽  
Kyle J. Bibby ◽  
Daniel S. Jones ◽  
William D. Burgos ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Iron Oxidation ◽  
Cost Effective ◽  
Low Ph ◽  
Content Type ◽  
Oxidation Rates ◽  
Acid Mine

ABSTRACT Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens, a species that is associated with high rates of Fe(II) oxidation in laboratory studies. IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121–1123, 1970, https://doi.org/10.1126/science.167.3921.1121 ). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens, a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation.

scholarly journals Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Kyle C. Costa ◽  
Megan Bergkessel ◽  
Scott Saunders ◽  
Jonas Korlach ◽  
Dianne K. Newman
Keyword(s):  
Microbial Communities ◽  
Pathogenic Fungi ◽  
Cell Types ◽  
Redox Activity ◽  
Mycobacterium Fortuitum ◽  
Active Metabolites ◽  
Content Type ◽  
Phenazine Production ◽  
Physiological Benefits

ABSTRACTDiverse bacteria, including severalPseudomonasspecies, produce a class of redox-active metabolites called phenazines that impact different cell types in nature and disease. Phenazines can affect microbial communities in both positive and negative ways, where their presence is correlated with decreased species richness and diversity. However, little is known about how the concentration of phenazines is modulatedin situand what this may mean for the fitness of members of the community. Through culturing of phenazine-degrading mycobacteria, genome sequencing, comparative genomics, and molecular analysis, we identified several conserved genes that are important for the degradation of threePseudomonas-derived phenazines: phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and pyocyanin (PYO). PCA can be used as the sole carbon source for growth by these organisms. Deletion of several genes inMycobacterium fortuitumabolishes the degradation phenotype, and expression of two genes in a heterologous host confers the ability to degrade PCN and PYO. In cocultures with phenazine producers, phenazine degraders alter the abundance of different phenazine types. Not only does degradation support mycobacterial catabolism, but also it provides protection to bacteria that would otherwise be inhibited by the toxicity of PYO. Collectively, these results serve as a reminder that microbial metabolites can be actively modified and degraded and that these turnover processes must be considered when the fate and impact of such compounds in any environment are being assessed.IMPORTANCEPhenazine production byPseudomonasspp. can shape microbial communities in a variety of environments ranging from the cystic fibrosis lung to the rhizosphere of dryland crops. For example, in the rhizosphere, phenazines can protect plants from infection by pathogenic fungi. The redox activity of phenazines underpins their antibiotic activity, as well as providing pseudomonads with important physiological benefits. Our discovery that soil mycobacteria can catabolize phenazines and thereby protect other organisms against phenazine toxicity suggests that phenazine degradation may influence turnoverin situ. The identification of genes involved in the degradation of phenazines opens the door to monitoring turnover in diverse environments, an essential process to consider when one is attempting to understand or control communities influenced by phenazines.

scholarly journals Iron Transformations Induced by an Acid-Tolerant Desulfosporosinus Species

2011 ◽  
Vol 78 (1) ◽  
pp. 81-88 ◽  
Author(s):  
Doug Bertel ◽  
John Peck ◽  
Thomas J. Quick ◽  
John M. Senko
Keyword(s):  
Mine Drainage ◽  
Low Ph ◽  
Content Type ◽  
X Ray ◽  
First Order ◽  
Geochemical Conditions ◽  
Sulfate Reducing ◽  
Mineral Phases ◽  
Magnetic Analysis ◽  
Acid Tolerant

ABSTRACTThe mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium,Desulfosporosinussp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe3S4) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe8O8(OH)6SO4·nH2O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2.

scholarly journals Microbial Communities on Plastic Polymers in the Mediterranean Sea

2021 ◽  
Vol 12 ◽  
Author(s):  
Annika Vaksmaa ◽  
Katrin Knittel ◽  
Alejandro Abdala Asbun ◽  
Maaike Goudriaan ◽  
Andreas Ellrott ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mediterranean Sea ◽  
Amplicon Sequencing ◽  
Polymer Surfaces ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Microbial Biofilms ◽  
Degrading Bacteria ◽  
The Mediterranean

Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating microplastics in a bay of the island of Elba in the Mediterranean Sea. Raman spectroscopy revealed that the plastic particles mainly comprised polyethylene (PE), polypropylene (PP), and polystyrene (PS) of which polyethylene and polypropylene particles were typically brittle and featured cracks. Fluorescence in situ hybridization and imaging by high-resolution microscopy revealed dense microbial biofilms on the polymer surfaces. Amplicon sequencing of the 16S rRNA gene showed that the bacterial communities on all plastic types consisted mainly of the orders Flavobacteriales, Rhodobacterales, Cytophagales, Rickettsiales, Alteromonadales, Chitinophagales, and Oceanospirillales. We found significant differences in the biofilm community composition on PE compared with PP and PS (on OTU and order level), which shows that different microbial communities colonize specific polymer types. Furthermore, the sequencing data also revealed a higher relative abundance of archaeal sequences on PS in comparison with PE or PP. We furthermore found a high occurrence, up to 17% of all sequences, of different hydrocarbon-degrading bacteria on all investigated plastic types. However, their functioning in the plastic-associated biofilm and potential role in plastic degradation needs further assessment.

scholarly journals Quantitative detection of isotopically enrichedE. colicells by SERS

2017 ◽  
Vol 205 ◽  
pp. 331-343 ◽  
Author(s):  
Malama Chisanga ◽  
Howbeer Muhamadali ◽  
Richard Kimber ◽  
Royston Goodacre
Keyword(s):  
Microbial Communities ◽  
Municipal Wastewater ◽  
Stable Isotope Probing ◽  
Quantitative Detection ◽  
Raman Signal ◽  
Spectroscopic Techniques ◽  
Bacterial Cells ◽  
Least Squares Regression ◽  
Municipal Wastewater Treatment

It is clear that investigating how bacterial cells work by analysing their functional roles in microbial communities is very important in environmental, clinical and industrial microbiology. The benefits of linking genes to their respective functions include the reliable identification of the causative agents of various diseases, which would permit appropriate and timely treatment in healthcare systems. In industrial and municipal wastewater treatment and management, such knowledge may allow for the manipulation of microbial communities, such as through bioaugmentation, in order to improve the efficiency and effectiveness of bioremediation processes. Stable isotope probing coupled with identification techniques has emerged to be a potentially reliable tool for the discrimination, identification and characterization of bacteria at community and single cell levels, knowledge which can be utilized to link microbially mediated bioprocesses to phylogeny. Development of the surface-enhanced Raman scattering (SERS) technique offers an exciting alternative to the Raman and Fourier-transform infrared spectroscopic techniques in understanding the metabolic processes of microorganismsin situ. SERS employing Ag and Au nanoparticles can significantly enhance the Raman signal, making it an exciting candidate for the analysis of the cellular components of microorganisms. In this study,Escherichia colicells were cultivated in minimal medium containing different ratios of12C/13C glucose and/or14N/15N ammonium chloride as the only carbon and nitrogen sources respectively, with the overall final concentrations of these substrates being constant. After growth, theE. colicells were analyzed with SERS employing anin situsynthesis of Ag nanoparticles. This novel investigation of the SERS spectral data with multivariate chemometrics demonstrated clear clusters which could be correlated to the SERS spectral shifts of biomolecules from cells grown and hence labelled with13C and15N atoms. These shifts reflect the isotopic content of the bacteria and quantification of the isotope levels could be established using chemometrics based on partial least squares regression.

scholarly journals In SituBiomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine

2016 ◽  
Vol 82 (10) ◽  
pp. 2886-2892 ◽  
Author(s):  
Xiaobao Li ◽  
David L. Chopp ◽  
William A. Russin ◽  
Paul T. Brannon ◽  
Matthew R. Parsek ◽  
...  
Keyword(s):  
Particle Deposition ◽  
Transport Processes ◽  
Mineral Deposits ◽  
Mineral Formation ◽  
Fluorescent Tracer ◽  
Content Type ◽  
Microbial Biofilms ◽  
Essential Properties ◽  
Internal Transport

ABSTRACTMicrobial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed thatin situbiomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show thatPseudomonas aeruginosabiofilms are more permeable to solutes afterin situcalcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects ofin situbiomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control.

scholarly journals Application of a DepositionalFaciesModel to an Acid Mine Drainage Site

2010 ◽  
Vol 77 (2) ◽  
pp. 545-554 ◽  
Author(s):  
Juliana F. Brown ◽  
Daniel S. Jones ◽  
Daniel B. Mills ◽  
Jennifer L. Macalady ◽  
William D. Burgos
Keyword(s):  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Low Ph ◽  
Strongly Correlated ◽  
Microbial Composition ◽  
Geochemical Conditions ◽  
Oxidation Rates ◽  
Acid Mine ◽  
Red Eyes

ABSTRACTLower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a depositionalfaciesmodel. Depositionalfacieswere defined as pools, terraces, or microterracettes based on cm-scale sediment morphology, irrespective of the distance downstream from the spring. The sediments were composed entirely of Fe precipitates and cemented organic matter. The Fe precipitates were identified as schwertmannite at all locations, regardless offacies. Microbial composition was studied with fluorescencein situhybridization (FISH) and transitioned from a microaerophilic,Euglena-dominated community at the spring, to aBetaproteobacteria(primarilyFerrovumspp.)-dominated community at the upstream end of the iron mound, to aGammaproteobacteria(primarilyAcidithiobacillus)-dominated community at the downstream end of the iron mound. Microbial community structure was more strongly correlated with pH and geochemical conditions than depositionalfacies. Intact pieces of terrace and pool sediments from upstream and downstream locations were used in flowthrough laboratory reactors to measure the rate and extent of low-pH Fe(II) oxidation. No change in Fe(II) concentration was observed with60Co-irradiated sediments or with no-sediment controls, indicating that abiotic Fe(II) oxidation was negligible. Upstream sediments attained lower effluent Fe(II) concentrations compared to downstream sediments, regardless of depositionalfacies.

scholarly journals Novel Clade of Alphaproteobacterial Endosymbionts Associated with Stinkbugs and Other Arthropods

2012 ◽  
Vol 78 (12) ◽  
pp. 4149-4156 ◽  
Author(s):  
Yu Matsuura ◽  
Yoshitomo Kikuchi ◽  
Xian Ying Meng ◽  
Ryuichi Koga ◽  
Takema Fukatsu
Keyword(s):  
Gene Sequence ◽  
Rrna Gene ◽  
Bacterial Cells ◽  
Anterior Pole ◽  
Rrna Gene Sequence ◽  
Detection Rates ◽  
Diagnostic Pcr ◽  
Content Type ◽  
Molecular Phylogenetic

ABSTRACTHere we report a novel clade of secondary endosymbionts associated with insects and other arthropods. Seed bugs of the genusNysius(Hemiptera: Lygaeidae) harbor the primary gammaproteobacterial symbiontSchneideria nysicolawithin a pair of bacteriomes in the abdomen. Our survey ofNysiusspecies for their facultative bacterial associates consistently yielded a novel type of alphaproteobacterial 16S rRNA gene sequence in addition to those ofWolbachia. Diagnostic PCR survey of 343 individuals representing 24 populations of fourNysiusspecies revealed overall detection rates of the alphaproteobacteria at 77.6% inNysius plebeius, 87.7% inNysiussp. 1, 81.0% inNysiussp. 2, and 100% inNysius expressus. Further survey of diverse stinkbugs representing 24 families, 191 species, and 582 individuals detected the alphaproteobacteria from an additional 12 species representing six families. Molecular phylogenetic analysis showed that the alphaproteobacteria from the stinkbugs form a distinct and coherent monophyletic group in the orderRickettsialestogether with several uncharacterized endosymbionts from fleas and ticks. The alphaproteobacterial symbiont clade was allied to bacterial clades such as the endosymbionts of acanthamoebae, the endosymbionts of cnidarians, andMidichloriaspp., the mitochondrion-associated endosymbionts of ticks.In situhybridization and electron microscopy identified small filamentous bacterial cells in various tissues ofN. plebeius, including the bacteriome and ovary. The concentrated localization of the symbiont cells at the anterior pole of oocytes indicated its vertical transmission route through host insect generations. The designation “CandidatusLariskella arthropodarum” is proposed for the endosymbiont clade.

scholarly journals Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages

2018 ◽  
Vol 628-629 ◽  
pp. 26-35 ◽  
Author(s):  
Thomas Coral ◽  
Michaël Descostes ◽  
Hélène De Boissezon ◽  
Rizlan Bernier-Latmani ◽  
Luiz Felippe de Alencastro ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Acid Mine ◽  
In Situ Recovery
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