Microbial Community Structure in Midgut and Hindgut of the Humus-Feeding Larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae)

ABSTRACT The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and Cytophaga-Flavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae.

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Effects of Heavy Fuel Oil on the Bacterial Community Structure of a Pristine Microbial Mat

Applied and Environmental Microbiology ◽

10.1128/aem.01352-07 ◽

2007 ◽

Vol 73 (19) ◽

pp. 6089-6097 ◽

Cited By ~ 101

Author(s):

Sylvain Bordenave ◽

María Soledad Goñi-Urriza ◽

Pierre Caumette ◽

Robert Duran

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rrna ◽

Oil Pollution ◽

Microbial Mat ◽

Fuel Oil ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Heavy Fuel Oil

ABSTRACT The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by “Bacilli” and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution.

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Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.569020 ◽

2021 ◽

Vol 12 ◽

Author(s):

Li Ma ◽

Geng Wu ◽

Jian Yang ◽

Liuqin Huang ◽

Dorji Phurbu ◽

...

Keyword(s):

Community Structure ◽

Hydrogen Production ◽

16S Rrna ◽

High Throughput Sequencing ◽

Hot Springs ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

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Anaerocolumna chitinilytica sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004999 ◽

2021 ◽

Vol 71 (9) ◽

Cited By ~ 4

Author(s):

Atsuko Ueki ◽

Akio Tonouchi ◽

Nobuo Kaku ◽

Katsuji Ueki

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Fermentation Products ◽

Content Type ◽

Soil Disinfestation ◽

Link Type ◽

The Family ◽

Genes Encoding

An obligately anaerobic bacterial strain (CTTWT) belonging to the family Lachnospiraceae within the class Clostridia was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan. Strain CTTWT decomposed cell biomass and cell-wall preparations of an ascomycete plant pathogen, Fusarium oxysporum f. sp. spinaciae. The strain produced acetate, ethanol, H2 and CO2 as fermentation products from the utilized substrates. The major cellular fatty acids of the strain were C16 : 1 ω7c dimethylacetal (DMA), C16 : 0 DMA and C18 : 1 ω7c DMA. The closely related species of strain CTTWT based on the 16S rRNA gene sequences were species in the genus Anaerocolumna with sequence similarities of 95.2–97.6 %. Results of genome analyses of strain CTTWT indicated that the genome size of the strain was 5.62 Mb and the genomic DNA G+C content was 38.3 mol%. Six 16S rRNA genes with five different sequences from each other were found in the genome. Strain CTTWT had genes encoding chitinase, xylanase, cellulase, β-glucosidase and nitrogenase as characteristic genes in the genome. Homologous genes encoding these proteins were found in the genomes of the related Anaerocolumna species, but the genomic and phenotypic properties of strain CTTWT were distinct from them. Based on the phylogenetic, genomic and phenotypic analyses, the name Anaerocolumna chitinilytica sp. nov., in the family Lachnospiraceae is proposed for strain CTTWT (=NBRC 112102T=DSM 110036T).

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Seasonal Variation of Microbial Diversity of Coastal Sediment in Tongyeong, South Korea, Using 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00446-21 ◽

2021 ◽

Vol 10 (27) ◽

Author(s):

Nur Indradewi Oktavitri ◽

Jong-Oh Kim ◽

Kyunghoi Kim

Keyword(s):

Seasonal Variation ◽

Microbial Community ◽

16S Rrna ◽

South Korea ◽

Microbial Diversity ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Generation Sequencing

Benthic microbial diversity in Tongyeong, South Korea, was analyzed using next-generation sequencing of the 16S rRNA genes, to reveal the effects of seasonal variations on the microbial community in sediment. Proteobacteria was the dominant phylum, with a relative abundance of 61.5 to 68.1%.

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Description of Oceanispirochaeta crateris sp. nov. and reclassification of Spirochaeta perfilievii as Thiospirochaeta perfilievii gen. nov., comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004544 ◽

2020 ◽

Vol 70 (12) ◽

pp. 6373-6380 ◽

Cited By ~ 8

Author(s):

Galina Dubinina ◽

Natalia Leshcheva ◽

Natalia Mikheeva ◽

Stefan Spring ◽

Meina Neumann-Schaal ◽

...

Keyword(s):

16S Rrna ◽

Type Species ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Fermentation Products ◽

Content Type ◽

Link Type

A novel obligately anaerobic spirochete strain K2T was isolated from bottom marine sediments at Crater Bay of Yankicha Island (Kuril Islands, Russia). Strain K2T had helical shape and Gram-negatively stained. The optimal growth conditions were as follows: the optimum temperature was 28–30 °C with range 5–34 °C; optimal pH at 7.0–7.5 with range of 6.8–8.5; NaCl optimum at 3–3.5 % (w/v) and range of 1–7 % (w/v). Strain K2T was catalase- and oxidase-negative. Glucose fermentation products were acetate, lactate, ethanol, CO2, H2. The major fatty acids were C14 : 0, iso-C13 : 0, iso-C15:0, C14 : 0 DMA, iso-C15 : 0 DMA. The G+C content of genomic DNA was 43.2 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain K2T belonged to the genus Oceanispirochaeta of the family Spirochaetaceae . The 16S rRNA gene sequence similarity of strain K2T and O. litoralis DSM 2029T and O. sediminicola DSM 104770T was 96 and 94 %, respectively. Based on the results of our study, we propose the name Oceanispirochaeta crateris sp. nov.; type strain K2T (=DSM 16308T=VKM B-3266T). Also, the taxonomic status of Spirochaeta perfilevii was revised: 16S rRNA genes sequence showed less than 89 % similarity to nearest phylogenetic neighbours. Therefore, we proposed to separate this species into a novel genus Thiospirochaeta - T. perfilievii gen. nov., comb. nov.

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Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions

Applied and Environmental Microbiology ◽

10.1128/aem.01986-15 ◽

2015 ◽

Vol 81 (20) ◽

pp. 7114-7124 ◽

Cited By ~ 9

Author(s):

Kenly A. Hiller ◽

Kenneth H. Foreman ◽

David Weisman ◽

Jennifer L. Bowen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Bacterial Community Composition ◽

Environmental Parameters ◽

Permeable Reactive Barriers ◽

16S Rrna Genes ◽

Rrna Genes ◽

Reactive Barriers

ABSTRACTPermeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole.

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Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework

PeerJ ◽

10.7717/peerj.6496 ◽

2019 ◽

Vol 7 ◽

pp. e6496 ◽

Cited By ~ 17

Author(s):

Gemma Henderson ◽

Pelin Yilmaz ◽

Sandeep Kumar ◽

Robert J. Forster ◽

William J. Kelly ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Rumen Bacteria ◽

Genus Level ◽

Bacterial 16S Rrna Gene

The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.

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Acidianus Brierleyi is the Dominant Thermoacidophile in a Bioleaching Community Processing Chalcopyrite Containing Concentrates at 70°C

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.71-73.67 ◽

2009 ◽

Vol 71-73 ◽

pp. 67-70 ◽

Cited By ~ 11

Author(s):

Inez J.T. Dinkla ◽

Mariekie Gericke ◽

B.K. Geurkink ◽

Kevin B. Hallberg

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Clone Library ◽

Rflp Analysis ◽

16S Rrna Genes ◽

Qualitative Assessment ◽

Rrna Genes ◽

Rrna Gene ◽

Multi Stage ◽

Acidianus Brierleyi

Bioleaching test work was performed in continuously operated multi-stage reactor systems at 70°C using a thermophilic culture treating an Aguablanca Ni-Cu concentrate from Spain and a blend of Cu concentrates from Bor, Serbia. The copper in both these concentrates occurs as chalcopyrite and therefore the use of thermophiles was applied, which resulted in copper recoveries of over 95%. Qualitative assessment of the microbial community in the bioreactors was performed by terminal restriction enzyme fragment length polymorphism (T-RFLP) and clone library analysis of the 16S rRNA genes amplified by PCR. T-RFLP analysis revealed that only archaea were present, and that the communities in both the Aguablanca and Bor systems consisted of two different microorganisms. A 16S rRNA gene clone library using DNA from the Aguablanca system was constructed and screened. Again, two archaea were detected in similar relative abundance in the population as found by T-RFLP analyses. The sequences of these two cloned genes revealed that the dominant archaeon (up to 98% of the total archaea detected) was Acidianus brierleyi, and the other was Metallosphaera sedula. Quantitative assessment of the microbial community was performed by Q-PCR and confirmed the dominance of archaea in the system with Acidianus being the dominant strain (98-99% of the total population) and a minor part of the population (1-2%) consisted of Metallosphaera. Additionally, very small amounts of Sulfolobus spp. were detected. This study, along with other recent studies on the diversity of thermoacidophiles involved in the solubilization of copper from chalcopyrite concentrates, revealed that a wider variety of thermoacidophiles are involved in bioprocessing of metal sulfides, and showed that A. brierleyi should be considered an important biomining acidophile.

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Spatial and Temporal Analysis of the Microbial Community in Slow Sand Filters Used for Treating Horticultural Irrigation Water

Applied and Environmental Microbiology ◽

10.1128/aem.69.4.2116-2125.2003 ◽

2003 ◽

Vol 69 (4) ◽

pp. 2116-2125 ◽

Cited By ~ 50

Author(s):

Leo A. Calvo-Bado ◽

Tim R. Pettitt ◽

Nick Parsons ◽

Geoff M. Petch ◽

J. Alun W. Morgan ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Plant Pathogen ◽

Temporal Structure ◽

16S Rrna Genes ◽

Rrna Genes ◽

Global Changes ◽

Rrna Gene ◽

Microbial Composition

ABSTRACT An experimental slow sand filter (SSF) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, Phytophthora cryptogea. Passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. To monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the ATP content was measured. PCR amplification of 16S rRNA genes and denaturing gradient gel electrophoresis (DGGE) were used to study the dynamics of the bacterial community in detail. The top layer (1 cm) of the SSF column was dominated by a variable and active microbial population, whereas the middle (50 cm) and bottom (80 cm) layers were dominated by less active and diverse bacterial populations. The major changes in the microbial populations occurred during the first week of filter operation, and these populations then remained to the end of the study. Spatial and temporal nonlinear mapping of the DGGE bands provided a useful visual representation of the similarities between SSF samples. According to the DGGE profile, less than 2% of the dominating bands present in the SSF column were represented in the culturable population. Sequence analysis of DGGE bands from all depths of the SSF column indicated that a range of bacteria were present, with 16S rRNA gene sequences similar to groups such as Bacillus megaterium, Cytophaga, Desulfovibrio, Legionella, Rhodococcus rhodochrous, Sphingomonas, and an uncharacterized environmental clone. This study describes the characterization of the performance, and microbial composition, of SSFs used for the treatment of water for use in the horticultural industry. Utilization of naturally suppressive population of microorganisms either directly or by manipulation of the environment in an SSF may provide a more reproducible control method for the future.

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Isolation and Characterization of Novel Marine-Derived Actinomycete Taxa Rich in Bioactive Metabolites

Applied and Environmental Microbiology ◽

10.1128/aem.70.12.7520-7529.2004 ◽

2004 ◽

Vol 70 (12) ◽

pp. 7520-7529 ◽

Cited By ~ 149

Author(s):

Nathan A. Magarvey ◽

Jessica M. Keller ◽

Valerie Bernan ◽

Martin Dworkin ◽

David H. Sherman

Keyword(s):

16S Rrna ◽

Multidrug Resistant ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bioactive Metabolites ◽

Rrna Gene ◽

New Genera ◽

Isolation And Identification ◽

Fermentation Products ◽

Isolation And Characterization

ABSTRACT A unique selective enrichment procedure has resulted in the isolation and identification of two new genera of marine-derived actinobacteria. Approximately 90% of the microorganisms cultured by using the presented method were from the prospective new genera, a result indicative of its high selectivity. In this study, 102 actinomycetes were isolated from subtidal marine sediments collected from the Bismarck Sea and the Solomon Sea off the coast of Papua New Guinea. A combination of physiological parameters, chemotaxonomic characteristics, distinguishing 16S rRNA gene sequences, and phylogenetic analysis based on 16S rRNA genes provided strong evidence for the two new genera (represented by strains of the PNG1 clade and strain UMM518) within the family Micromonosporaceae. Biological activity testing of fermentation products from the new marine-derived actinomycetes revealed that several had activities against multidrug-resistant gram-positive pathogens, malignant cells, and vaccinia virus replication.

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