scholarly journals Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats

2015 ◽  
Vol 82 (2) ◽  
pp. 650-658 ◽  
Author(s):  
Brooke L. Weigel ◽  
Patrick M. Erwin
Keyword(s):  
Microbial Communities ◽  
Host Specificity ◽  
Intraspecific Variation ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Ambient Seawater ◽  
Air Exposure ◽  
Content Type ◽  
Ideal System ◽  
Microbial Symbiont

ABSTRACTSponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidalHymeniacidonheliophilasponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared toH. heliophilasymbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found inH. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses.

scholarly journals Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

2012 ◽  
Vol 78 (21) ◽  
pp. 7527-7537 ◽  
Author(s):  
David R. Andrew ◽  
Robert R. Fitak ◽  
Adrian Munguia-Vega ◽  
Adriana Racolta ◽  
Vincent G. Martinson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Sonoran Desert ◽  
Abiotic Factors ◽  
Extreme Environments ◽  
Community Diversity ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Phyla ◽  
Culture Independent

ABSTRACTHigh-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundantCrenarchaeotaclassThermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phylaProteobacteria,Actinobacteria,Planctomycetes,Firmicutes,Bacteroidetes,Chloroflexi, andAcidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Extracellular Enzyme Activity and Microbial Diversity Measured on Seafloor Exposed Basalts from Loihi Seamount Indicate the Importance of Basalts to Global Biogeochemical Cycling

2014 ◽  
Vol 80 (16) ◽  
pp. 4854-4864 ◽  
Author(s):  
Myrna E. Jacobson Meyers ◽  
Jason B. Sylvan ◽  
Katrina J. Edwards
Keyword(s):  
Enzyme Activity ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Leucine Aminopeptidase ◽  
Extracellular Enzyme ◽  
Basaltic Rock ◽  
Rrna Gene ◽  
Content Type ◽  
Shelf Sediments ◽  
Potential Enzyme Activity

ABSTRACTSeafloor basalts are widely distributed and host diverse prokaryotic communities, but no data exist concerning the metabolic rates of the resident microbial communities. We present here potential extracellular enzyme activities of leucine aminopeptidase (LAP) and alkaline phosphatase (AP) measured on basalt samples from different locations on Loihi Seamount, HI, coupled with analysis of prokaryotic biomass and pyrosequencing of the bacterial 16S rRNA gene. The community maximum potential enzyme activity (Vmax) of LAP ranged from 0.47 to 0.90 nmol (g rock)−1h−1; theVmaxfor AP was 28 to 60 nmol (g rock)−1h−1. TheKmof LAP ranged from 26 to 33 μM, while theKmfor AP was 2 to 7 μM. Bacterial communities on Loihi basalts were comprised primarily ofAlpha-,Delta-, andGammaproteobacteria,Bacteroidetes, andPlanctomycetes. The putative ability to produce LAP is evenly distributed across the most commonly detected bacterial orders, but the ability to produce AP is likely dominated by bacteria in the ordersXanthomonadales,Flavobacteriales, andPlanctomycetales. The enzyme activities on Loihi basalts were compared to those of other marine environments that have been studied and were found to be similar in magnitude to those from continental shelf sediments and orders of magnitude higher than any measured in the water column, demonstrating that the potential for exposed basalts to transform organic matter is substantial. We propose that microbial communities on basaltic rock play a significant, quantifiable role in benthic biogeochemical processes.

scholarly journals Repeated Anaerobic Microbial Redox Cycling of Iron

2011 ◽  
Vol 77 (17) ◽  
pp. 6036-6042 ◽  
Author(s):  
Aaron J. Coby ◽  
Flynn Picardal ◽  
Evgenya Shelobolina ◽  
Huifang Xu ◽  
Eric E. Roden
Keyword(s):  
Microbial Communities ◽  
Microscopic Analysis ◽  
Redox Cycling ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Electron Microscopic ◽  
16S Rrna Gene Analysis ◽  
Probable Number ◽  
Content Type ◽  
Floodplain Sediments

ABSTRACTSome nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifyingBetaproteobacteria(e.g.,Dechloromonas) and Fe(III)-reducingDeltaproteobacteria(Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that bothGeobacterand variousBetaproteobacteriaparticipated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments.

scholarly journals Microbial Community Stratification Controlled by the Subseafloor Fluid Flow and Geothermal Gradient at the Iheya North Hydrothermal Field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)

2014 ◽  
Vol 80 (19) ◽  
pp. 6126-6135 ◽  
Author(s):  
Katsunori Yanagawa ◽  
Anja Breuker ◽  
Axel Schippers ◽  
Manabu Nishizawa ◽  
Akira Ijiri ◽  
...  
Keyword(s):  
Fluid Flow ◽  
Microbial Communities ◽  
Okinawa Trough ◽  
Geothermal Gradient ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Ocean Drilling Program ◽  
Content Type ◽  
Ocean Drilling ◽  
Integrated Ocean Drilling Program

ABSTRACTThe impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of theChloroflexiand deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group IThaumarchaeotadominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments.

scholarly journals Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass

2014 ◽  
Vol 80 (23) ◽  
pp. 7423-7432 ◽  
Author(s):  
Stephanie A. Eichorst ◽  
Chijioke Joshua ◽  
Noppadon Sathitsuksanoh ◽  
Seema Singh ◽  
Blake A. Simmons ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Biomass ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Gravimetric Analysis ◽  
Content Type ◽  
Biomass Deconstruction ◽  
Bacterial Consortia ◽  
Residual Biomass ◽  
Chemical Pretreatments

ABSTRACTMicrobial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of theFirmicutes, theBacteroidetes, andDeinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.

scholarly journals Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments

2012 ◽  
Vol 78 (22) ◽  
pp. 7856-7865 ◽  
Author(s):  
Chiachi Hwang ◽  
Fangqiong Ling ◽  
Gary L. Andersen ◽  
Mark W. LeChevallier ◽  
Wen-Tso Liu
Keyword(s):  
Drinking Water ◽  
Microbial Community ◽  
Microbial Communities ◽  
Distribution Systems ◽  
Water Distribution ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Source Water ◽  
Content Type ◽  
Drinking Water Distribution

ABSTRACTWater utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations,Cyanobacteria,Methylobacteriaceae,Sphingomonadaceae, andXanthomonadaceaewere more abundant in chlorinated water, andMethylophilaceae,Methylococcaceae, andPseudomonadaceaewere more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations includingFlavobacteriaceaeandClostridiaceaewere also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

scholarly journals Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA

2014 ◽  
Vol 80 (11) ◽  
pp. 3518-3530 ◽  
Author(s):  
Xueju Lin ◽  
Malak M. Tfaily ◽  
J. Megan Steinweg ◽  
Patrick Chanton ◽  
Kaitlin Esson ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Hot Spot ◽  
Microbial Community Composition ◽  
Phosphorus Limitation ◽  
Rrna Gene ◽  
Content Type ◽  
Gene Abundance ◽  
P Limitation

ABSTRACTThis study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance ofAcidobacteriaand theSyntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance ofArchaea(primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by theMethanosarcinalesin the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub,Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.

scholarly journals Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients

2016 ◽  
Vol 82 (22) ◽  
pp. 6633-6644 ◽  
Author(s):  
Francesco Paroni Sterbini ◽  
Alessandra Palladini ◽  
Luca Masucci ◽  
Carlo Vittorio Cannistraci ◽  
Roberta Pastorino ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Proton Pump Inhibitors ◽  
Proton Pump ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Content Type ◽  
Treatment Regimens ◽  
H Pylori ◽  
Content Status ◽  
Gastric Microbiota

ABSTRACTBesides being part of anti-Helicobacter pyloritreatment regimens, proton pump inhibitors (PPIs) are increasingly being used to treat dyspepsia. However, little is known about the effects of PPIs on the human gastric microbiota, especially those related toH. pyloriinfection. The goal of this study was to characterize the stomach microbial communities in patients with dyspepsia and to investigate their relationships with PPI use andH. pyloristatus. Using 16S rRNA gene pyrosequencing, we analyzed the mucosa-associated microbial populations of 24 patients, of whom 12 were treated with the PPI omeprazole and 9 (5 treated and 4 untreated) were positive forH. pyloriinfection. TheProteobacteria,Firmicutes,Bacteroidetes,Fusobacteria, andActinobacteriaphyla accounted for 98% of all of the sequences, withHelicobacter,Streptococcus, andPrevotellaranking among the 10 most abundant genera.H. pyloriinfection or PPI treatment did not significantly influence gastric microbial species composition in dyspeptic patients. Principal-coordinate analysis of weighted UniFrac distances in these communities revealed clear but significant separation according toH. pyloristatus only. However, in PPI-treated patients,Firmicutes, particularlyStreptococcaceae, were significantly increased in relative abundance compared to those in untreated patients. Consistently,Streptococcuswas also found to significantly increase in relation to PPI treatment, and this increase seemed to occur independently ofH. pyloriinfection. Our results suggest thatStreptococcusmay be a key indicator of PPI-induced gastric microbial composition changes in dyspeptic patients. Whether the gastric microbiota alteration contributes to dyspepsia needs further investigation.IMPORTANCEAlthough PPIs have become a popular treatment choice, a growing number of dyspeptic patients may be treated unnecessarily. We found that patients treated with omeprazole showed gastric microbial communities that were different from those of untreated patients. These differences regarded the abundances of specific taxa. By understanding the relationships between PPIs and members of the gastric microbiota, it will be possible to envisage new strategies for better managing patients with dyspepsia.

scholarly journals Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

2015 ◽  
Vol 81 (22) ◽  
pp. 7924-7937 ◽  
Author(s):  
Christopher E. Lawson ◽  
Cameron R. Strachan ◽  
Dominique D. Williams ◽  
Susan Koziel ◽  
Steven J. Hallam ◽  
...  
Keyword(s):  
Habitat Selection ◽  
Microbial Communities ◽  
Coalbed Methane ◽  
Alternative Energy ◽  
Nitrogen Availability ◽  
Energy Resource ◽  
Rrna Gene ◽  
Content Type ◽  
Wide Range ◽  
Alberta Basin

ABSTRACTMicrobially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated byRhodobacteraceaegenotypes, resolving a near-complete population genome bin related toCeleribactersp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between theCeleribactersp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.

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