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 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 Comparison of Extracellular Enzyme Activities and Community Composition of Attached and Free-Living Bacteria in Porous Medium Columns

2002 ◽  
Vol 68 (4) ◽  
pp. 1569-1575 ◽  
Author(s):  
R. Michael Lehman ◽  
Seán P. O'Connell
Keyword(s):  
Porous Medium ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Solid Phase ◽  
Pcr Amplification ◽  
Extracellular Enzyme ◽  
Free Living ◽  
Extracellular Enzyme Activities ◽  
Community Function

ABSTRACT Free-living and surface-associated microbial communities in sand-packed columns perfused with groundwater were compared by examination of compositional and functional characteristics. The composition of the microbial communities was assessed by bulk DNA extraction, PCR amplification of 16S ribosomal DNA fragments, separation of these fragments by denaturing gradient gel electrophoresis, and sequence analysis. Community function was assessed by measurement of β-glucosidase and aminopeptidase extracellular enzyme activities. Free-living populations in the aqueous phase exhibited a greater diversity of phylotypes than populations associated with the solid phase. The attached bacterial community displayed significantly greater β-glucosidase and aminopeptidase enzyme activities per volume of porous medium than those of the free-living community. On a per-cell basis, the attached community had a significantly higher cell-specific aminopeptidase enzyme activity (1.07 × 10−7 nmol cell−1 h−1) than the free-living community (5.02 × 10−8 nmol cell−1 h−1). Conversely, the free-living community had a significantly higher cell-specific β-glucosidase activity (1.92 × 10−6 nmol cell−1 h−1) than the surface-associated community (6.08 × 10−7 nmol cell−1 h−1). The compositional and functional differences observed between these two communities may reflect different roles for these distinct but interacting communities in the decomposition of natural organic matter or biodegradation of xenobiotics in aquifers.

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.

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