scholarly journals Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the 13C Content of Bacterial rRNA

2007 ◽  
Vol 74 (4) ◽  
pp. 1157-1166 ◽  
Author(s):  
Ann Pearson ◽  
Kimberly S. Kraunz ◽  
Alex L. Sessions ◽  
Anne E. Dekas ◽  
William D. Leavitt ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Petroleum Hydrocarbons ◽  
Oil Spills ◽  
Bacterial Biomass ◽  
Magnetic Bead ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Carbon Isotopic ◽  
Microbial Utilization

ABSTRACT Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids.

scholarly journals Distribution and Diversity of Archaeal and Bacterial Ammonia Oxidizers in Salt Marsh Sediments

2009 ◽  
Vol 75 (23) ◽  
pp. 7461-7468 ◽  
Author(s):  
Nicole S. Moin ◽  
Katelyn A. Nelson ◽  
Alexander Bush ◽  
Anne E. Bernhard
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
New England ◽  
Water Column ◽  
Salt Marshes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Group I ◽  
Marsh Sediments ◽  
Salt Marsh Sediments

ABSTRACT Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA amoA sequences at SAS were primarily affiliated with the water column/sediment clade. At all three site types, AOA were always more abundant than β-AOB based on quantitative PCR of amoA genes. At some sites, we detected 109 AOA amoA gene copies g of sediment−1. Ratios of AOA to β-AOB varied over 2 orders of magnitude among sites and sampling dates. Nevertheless, abundances of AOA and β-AOB amoA genes were highly correlated. Abundance of 16S rRNA genes affiliated with Nitrosopumilus maritimus, Crenarchaeota group I.1b, and pSL12 were positively correlated with AOA amoA abundance, but ratios of amoA to 16S rRNA genes varied among sites. We also observed a significant effect of pH on AOA abundance and a significant salinity effect on both AOA and β-ΑΟΒ abundance. Our results expand the distribution of AOA to salt marshes, and the high numbers of AOA at some sites suggest that salt marsh sediments serve as an important habitat for AOA.

scholarly journals Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System

2005 ◽  
Vol 71 (10) ◽  
pp. 6134-6141 ◽  
Author(s):  
Eddie Cytryn ◽  
Jaap van Rijn ◽  
Andreas Schramm ◽  
Armin Gieseke ◽  
Dirk de Beer ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sulfide Oxidation ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Marine Aquaculture ◽  
Dgge Analysis ◽  
Dna And Rna ◽  
Gradient Gel Electrophoresis

ABSTRACT Bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus Thiomicrospira and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the Rhodobacteraceae (genera Roseobacter, Rhodobacter, and Rhodobium) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for Thauera-, Hydrogenophaga-, and Dethiosulfovibrio-like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet phylogenetically diverse microbial populations in nature.

scholarly journals Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

2012 ◽  
Vol 78 (12) ◽  
pp. 4200-4208 ◽  
Author(s):  
Andrew J. Collins ◽  
Brenna A. LaBarre ◽  
Brian S. Wong Won ◽  
Monica V. Shah ◽  
Steven Heng ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Consortium ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Euprymna Scolopes ◽  
Sequencing Data ◽  
Content Type ◽  
Exact Function ◽  
Nidamental Gland

ABSTRACTMicrobial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid,Euprymna scolopes, a well-studied model organism for symbiosis research. Transmission electron microscopy (TEM) analysis of the ANG revealed dense bacterial assemblages of rod- and coccus-shaped cells segregated by morphology into separate, epithelium-lined tubules. The host epithelium was morphologically heterogeneous, containing ciliated and nonciliated cells with various brush border thicknesses. Hemocytes of the host's innate immune system were also found in close proximity to the bacteria within the tubules. A census of 16S rRNA genes suggested thatRhodobacterales, Rhizobiales, andVerrucomicrobiabacteria were prevalent, with members of the genusPhaeobacterdominating the consortium. Analysis of 454-shotgun sequencing data confirmed the presence of members of these taxa and revealed members of a fourth,Flavobacteriaof theBacteroidetesphylum. 16S rRNA fluorescentin situhybridization (FISH) revealed that many ANG tubules were dominated by members of specific taxa, namely,Rhodobacterales,Verrucomicrobia, orCytophaga-Flavobacteria-Bacteroidetes, suggesting symbiont partitioning to specific host tubules. In addition, FISH revealed that bacteria, includingPhaeobacterspecies from the ANG, are likely deposited into the jelly coat of freshly laid eggs. This report establishes the ANG of the invertebrateE. scolopesas a model to examine interactions between a bacterial consortium and its host.

scholarly journals Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

2021 ◽  
Author(s):  
Mingji Lu ◽  
Dominik Schneider ◽  
Rolf Daniel
Keyword(s):  
Markov Models ◽  
Sequence Similarity ◽  
Ecological Factors ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Lipolytic Enzymes ◽  
Two Samples ◽  
Metagenome Sequencing ◽  
Microbial Groups

AbstractLipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

scholarly journals Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass

2003 ◽  
Vol 69 (11) ◽  
pp. 6676-6687 ◽  
Author(s):  
Alison Buchan ◽  
Steven Y. Newell ◽  
Melissa Butler ◽  
Erin J. Biers ◽  
James T. Hollibaugh ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Rflp Analysis ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Natural Environments ◽  
Ecological Interactions ◽  
Decomposition Processes ◽  
Community Fingerprinting ◽  
Bacteria And Fungi

ABSTRACT Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the α-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the α-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate “4clt”).

scholarly journals The Diversity of Endophytic Methylotrophic Bacteria in an Oil-Contaminated and an Oil-Free Mangrove Ecosystem and Their Tolerance to Heavy Metals

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Manuella Nobrega Dourado ◽  
Anderson Ferreira ◽  
Welington Luiz Araújo ◽  
João Lúcio Azevedo ◽  
Paulo Teixeira Lacava
Keyword(s):  
Heavy Metals ◽  
Genetic Diversity ◽  
Oil Spills ◽  
Mangrove Ecosystem ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Methylotrophic Bacteria ◽  
Toxic Heavy Metal ◽  
Oil Components ◽  
Cadmium Lead

Methylobacterium strains were isolated from mangrove samples collected in Bertioga, SP, Brazil, from locations either contaminated or uncontaminated by oil spills. The tolerances of the strains to different heavy metals were assessed by exposing them to different concentrations of cadmium, lead, and arsenic (0.1 mM, 0.5 mM, 1 mM, 2 mM, 4 mM, and 8 mM). Additionally, the genetic diversity of Methylobacterium spp. was determined by sequence analysis of the 16S rRNA genes. The isolates from the contaminated locations were grouped, suggesting that oil can select for microorganisms that tolerate oil components and can change the methylotrophic bacterial community. Cadmium is the most toxic heavy metal assessed in this work, followed by arsenic and lead, and two isolates of Methylobacterium were found to be tolerant to all three metals. These isolates have the potential to bioremediate mangrove environments contaminated by oil spills by immobilizing the heavy metals present in the oil.

scholarly journals Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities

2019 ◽  
Vol 8 (1) ◽  
pp. 9
Author(s):  
Jack K. Beltz ◽  
Hayley McMahon ◽  
Isis Torres Nunez ◽  
Anne E. Bernhard
Keyword(s):  
Salt Marsh ◽  
Community Composition ◽  
Bacterial Abundance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
N Availability ◽  
Ammonia Oxidizing Archaea ◽  
Vegetation Zones ◽  
Total Bacterial Community

We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.

scholarly journals Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons

Water ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Rafaela Perdigão ◽  
C. Marisa R. Almeida ◽  
Filipa Santos ◽  
Maria F. Carvalho ◽  
Ana P. Mucha
Keyword(s):  
Petroleum Hydrocarbons ◽  
Oil Spills ◽  
Carbon Sources ◽  
Bacterial Biomass ◽  
Bacterial Consortium ◽  
Growth Conditions ◽  
Natural Seawater ◽  
Bacterial Strains ◽  
Beach Sediments ◽  
Insight Into

Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills.

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