Vertical Distribution of Methanogens in the Anoxic Sediment of Rotsee (Switzerland)

ABSTRACT Anoxic sediments from Rotsee (Switzerland) were analyzed for the presence and diversity of methanogens by using molecular tools and for methanogenic activity by using radiotracer techniques, in addition to the measurement of chemical profiles. After PCR-assisted sequence retrieval of the 16S rRNA genes (16S rDNA) from the anoxic sediment of Rotsee, cloning, and sequencing, a phylogenetic analysis identified two clusters of sequences and four separated clones. The sequences in cluster 1 grouped with those of Methanosaeta spp., whereas the sequences in cluster 2 comprised the methanogenic endosymbiont ofPlagiopyla nasuta. Discriminative oligonucleotide probes were constructed against both clusters and two of the separated clones. These probes were used subsequently for the analysis of indigenous methanogens in a core of the sediment, in addition to domain-specific probes against members of the domains Bacteria andArchaea and the fluorescent stain 4′,6-diamidino-2-phenylindole (DAPI), by fluorescent in situ hybridization. After DAPI staining, the highest microbial density was obtained in the upper sediment layer; this density decreased with depth from (1.01 ± 0.25) × 1010 to (2.62 ± 0.58) × 1010 cells per g of sediment (dry weight). This zone corresponded to that of highest metabolic activity, as indicated by the ammonia, alkalinity, and pH profiles, whereas the methane profile was constant. Probes Eub338 and Arch915 detected on average 16 and 6% of the DAPI-stained cells as members of the domains Bacteriaand Archaea, respectively. Probe Rotcl1 identified on average 4% of the DAPI-stained cells as Methanosaeta spp., which were present throughout the whole core. In contrast, probe Rotcl2 identified only 0.7% of the DAPI-stained cells as relatives of the methanogenic endosymbiont of P. nasuta, which was present exclusively in the upper 2 cm of the sediment. Probes Rotp13 and Rotp17 did not detect any cells. The spatial distribution of the two methanogenic populations corresponded well to the methane production rates determined by incubation with either [14C]acetate or [14C]bicarbonate. Methanogenesis from acetate accounted for almost all of the total methane production, which concurs with the predominance of acetoclastic Methanosaeta spp. that represented on average 91% of the archaeal population. Significant hydrogenotrophic methanogenesis was found only in the organically enriched upper 2 cm of the sediment, where the probably hydrogenotrophic relatives of the methanogenic endosymbiont of P. nasuta, accounting on average for 7% of the archaeal population, were also detected.

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ANME-1 archaea drive methane accumulation and removal in estuarine sediments

10.1101/2020.02.24.963215 ◽

2020 ◽

Cited By ~ 2

Author(s):

Richard Kevorkian ◽

Sean Callahan ◽

Rachel Winstead ◽

Karen G. Lloyd

Keyword(s):

16S Rrna ◽

Sulfate Reducing Bacteria ◽

Low Energy ◽

Estuarine Sediments ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sulfate Reducing ◽

Hydrogenotrophic Methanogenesis ◽

Natural Settings ◽

Reducing Bacteria

AbstractUncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide.Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

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Humin Assists Reductive Acetogenesis in Absence of Other External Electron Donor

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17124211 ◽

2020 ◽

Vol 17 (12) ◽

pp. 4211 ◽

Cited By ~ 1

Author(s):

Mahasweta Laskar ◽

Takuya Kasai ◽

Takanori Awata ◽

Arata Katayama

Keyword(s):

Carbon Source ◽

Electron Donor ◽

16S Rrna Genes ◽

Reductive Dehalogenation ◽

Rrna Genes ◽

Extracellular Electron Transfer ◽

Metagenomic Sequencing ◽

Electron Mediator ◽

Total Electron ◽

Methanogenic Activity

The utilization of extracellular electron transfer by microorganism is highly engaging for remediation of toxic pollutants under “energy-starved” conditions. Humin, an organo-mineral complex of soil, has been instrumental as an external electron mediator for suitable electron donors in the remediative works of reductive dehalogenation, denitrification, and so forth. Here, we report, for the first time, that humin assists microbial acetogenesis as the extracellular electron donor using the electron acceptor CO 2 . Humin was obtained from Kamajima paddy soil, Japan. The anaerobic acetogenic consortium in mineral medium containing CO 2 / HCO 3 − as the inorganic carbon source used suspended humin as the energy source under mesophilic dark conditions. Retardation of acetogenesis under the CO 2 -deficient conditions demonstrated that humin did not function as the organic carbon source but as electron donor in the CO 2 -reducing acetogenesis. The consortium with humin also achieved anaerobic dechlorination with limited methanogenic activity. Total electron-donating capacity of humin was estimated at about 87 µeeq/g-humin. The metagenomic sequencing of 16S rRNA genes showed the predominance of Firmicutes (71.8 ± 2.5%) in the consortium, and Lachnospiraceae and Ruminococcaceae were considered as the CO 2 -reducing acetogens in the consortium. Thus, microbial fixation of CO 2 using humin introduces new insight to the holistic approach for sustainable treatment of contaminants in environment.

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Characterization and Identification of Numerically Abundant Culturable Bacteria from the Anoxic Bulk Soil of Rice Paddy Microcosms

Applied and Environmental Microbiology ◽

10.1128/aem.65.11.5042-5049.1999 ◽

1999 ◽

Vol 65 (11) ◽

pp. 5042-5049 ◽

Cited By ~ 106

Author(s):

Kuk-Jeong Chin ◽

Dittmar Hahn ◽

Ulf Hengstmann ◽

Werner Liesack ◽

Peter H. Janssen

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dry Weight ◽

16S Rrna Genes ◽

Rrna Genes ◽

Most Probable Number ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Probable Number ◽

Clostridial Cluster

ABSTRACT Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 × 108 cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4′,6-diamidino-2-phenylindole staining, was 4.8 × 108cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the divisionVerrucomicrobia, theCytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050–5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.

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Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

Applied and Environmental Microbiology ◽

10.1128/aem.03640-15 ◽

2016 ◽

Vol 82 (8) ◽

pp. 2363-2371 ◽

Cited By ~ 37

Author(s):

Kaitlin C. Esson ◽

Xueju Lin ◽

Deepak Kumaresan ◽

Jeffrey P. Chanton ◽

J. Colin Murrell ◽

...

Keyword(s):

Dry Weight ◽

Amplicon Sequencing ◽

Stable Isotope Probing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Type I ◽

Type Ii ◽

Content Type ◽

Methane Consumption ◽

Field Samples

ABSTRACTThe objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil−1day−1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4%in situto 25 to 36% after 8 to 14 days. Phylogenetic analysis of the13C-enriched DNA fractions revealed that the active methanotrophs were dominated by the generaMethylocystis(type II;Alphaproteobacteria),Methylomonas, andMethylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed forpmoAin surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNApmoAamplicons from field samples confirmed that the dominant active methanotrophs wereMethylocystisandMethylomonas. Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the generaMethylomonasandMethylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.

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Thermal pretreatment of the solid fraction of manure: impact on the biogas reactor performance and microbial community

Water Science & Technology ◽

10.2166/wst.2006.236 ◽

2006 ◽

Vol 53 (8) ◽

pp. 59-67 ◽

Cited By ~ 42

Author(s):

Z. Mladenovska ◽

H. Hartmann ◽

T. Kvist ◽

M. Sales-Cruz ◽

R. Gani ◽

...

Keyword(s):

Microbial Community ◽

Solid Fraction ◽

Swine Manure ◽

16S Rrna Genes ◽

Rrna Genes ◽

Significant Activity ◽

Reactor Performance ◽

Methanogenic Activity ◽

Stirred Tank Reactors ◽

Biogas Reactor

Application of thermal treatment at 100–140 °C as a pretreatment method prior to anaerobic digestion of a mixture of cattle and swine manure was investigated. In a batch test, biogasification of manure with thermally pretreated solid fraction proceeded faster and resulted in the increase of methane yield. The performances of two thermophilic continuously stirred tank reactors (CSTR) treating manure with solid fraction pretreated for 40 minutes at 140 °C and non-treated manure were compared. The digester fed with the thermally pretreated manure had a higher methane productivity and an improved removal of the volatile solids (VS). The properties of microbial communities of both reactors were analysed. The specific methanogenic activity (SMA) test showed that both biomasses had significant activity towards hydrogen and formate, while the activity with the VFA – acetate, propionate and butyrate – was low. The kinetic parameters of the VFA conversion revealed a reduced affinity of the microbial community from the CSTR fed with thermally pre-treated manure for acetate, propionate and butyrate. The bacterial and archaeal populations identified by t-RLFP analysis of 16S rRNA genes were found to be identical in both systems. However, a change in the abundance of the species present was detected.

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Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats

10.1101/553032 ◽

2019 ◽

Cited By ~ 1

Author(s):

Julia M. McGonigle ◽

Jeremiah A. Bernau ◽

Brenda B. Bowen ◽

William J. Brazelton

Keyword(s):

Microbial Community ◽

Dna Sequencing ◽

Environmental Dna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sediment Layer ◽

Salt Flats ◽

Salt Crust ◽

Salt Pan ◽

Taxonomic Groups

ABSTRACTWe report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah–Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse Halobacteriaceae andSalinibacterspecies. Desulfuromonadales from GR-WP33-58 are also abundant in all samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. We found an increased presence of Thermoplasmatales, Nanohaloarchaeota, Woesearchaeota, Acetothermia, Halanaerobium, Parcubacteria, Planctomycetes, Clostridia, Gemmatimonadetes, Marinilabiaceae and other Bacteroidetes in this upper gypsum layer. This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically-sterile landscape.IMPORTANCEOver the last ∼13,000 years the Pleistocene Lake Bonneville, which covered a large portion of Utah, drained and desiccated leaving behind the Bonneville Salt Flats (BSF). Today BSF is famous for its use as a speedway, which has hosted many land-speed records and a community that greatly values this salty landscape. Additionally, the salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the roles of microbes in the formation and maintenance of the salt crust are generally unknown. This study is the first geospatial analysis of microbial diversity at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.

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Diversity Converges During Community Assembly In Methanogenic Granules, Suggesting A Biofilm Life-Cycle

10.1101/484642 ◽

2018 ◽

Cited By ~ 4

Author(s):

Anna Christine Trego ◽

Cristina Morabito ◽

Isabelle Bourven ◽

Gilles Guibaud ◽

Simon Mills ◽

...

Keyword(s):

Life Cycle ◽

Community Assembly ◽

Linear Convergence ◽

16S Rrna Genes ◽

Rrna Genes ◽

Core Microbiome ◽

Methanogenic Activity ◽

Size Fractions ◽

Physico Chemical ◽

Engineered Systems

Anaerobic biological decomposition of organic matter is ubiquitous in Nature wherever anaerobic environments prevail, and is catalysed by hydrolytic, fermentative, acetogenic, methanogenic, and various other groups, including syntrophic bacteria. It is also harnessed in innovative ways in engineered systems that may rely on small (0.1-4.0 mm), spherical, anaerobic granules, which we have found to be highly-replicated, whole-ecosystems harbouring the entire community necessary to mineralise complex organics. We hypothesised distinct granule sizes correspond to stages in a biofilm life-cycle, in which small granules are young and larger ones are old. Here, granules were separated into 10 size fractions used for physico-chemical and ecological characterisation. Gradients of volatile solids, density, settleability, biofilm morphology, methanogenic activity, and EPS profiles were observed across size fractions. Sequencing of 16S rRNA genes indicated linear convergence of diversity during community assembly as granules increased in size. A total of 155 discriminant OTUs were identified, and correlated strongly with physico-chemical parameters. Community assembly across sizes was influenced by a niche effect, whereby Euryarchaeota dominated a core microbiome presumably as granules became more anaerobic. The findings indicate opportunities for precision management of environmental biotechnologies, and the potential of aggregates as playgrounds to study assembly and succession in whole microbiomes.

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Vertical profiles of sediment methanogenic potential and communities in two plateau freshwater lakes

10.5194/bg-2016-321 ◽

2016 ◽

Author(s):

Yuyin Yang ◽

Bingxin Li ◽

Shuguang Xie ◽

Yong Liu

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Dianchi Lake ◽

Erhai Lake ◽

Sediment Layer ◽

Freshwater Lakes ◽

Layer Depth ◽

Change Pattern ◽

Archaeal Communities

Abstract. Microbial methanogenesis in sediment plays a crucial role in CH4 emission from freshwater lake ecosystem. However, knowledge on the layer depth-related changes of methanogens and their activities in freshwater lake sediment is still limited. The present study was conducted to characterize the methanogenesis potential in different sediment layer depths and the vertical distribution of microbial communities in two freshwater lakes at different trophic status on the Yunnan Plateau (China). Incubation experiments and inhibitor studies were carried out to determine the methanogenesis potential and pathways. McrA and 16S rRNA genes were used to investigate the abundance and structure of methanogen and archaeal communities, respectively. Hydrogenotrophic methanogenesis was mainly responsible for methane production in sediments of both freshwater lakes. The layer depth-related change pattern of the methanogenesis potential in Dianchi Lake was found to be different from that in Erhai Lake. mcrA and archaeal 16S rRNA genes displayed the similar abundance change pattern in either lake, and the relative abundance of methanogens decreased with increasing sediment layer depth. Archaeal communities differed considerably in Dianchi Lake and Erhai Lake, but methanogen communities showed a slight difference between in these two lakes. However, methanogen communities illustrated a remarkable layer depth-related change. Order Methanomicrobiales was the dominant methanogen group in all sediments, while Methanobacteriales showed high proportion only in upper layer sediments.

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Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats

mSphere ◽

10.1128/msphere.00378-19 ◽

2019 ◽

Vol 4 (4) ◽

Cited By ~ 3

Author(s):

Julia M. McGonigle ◽

Jeremiah A. Bernau ◽

Brenda B. Bowen ◽

William J. Brazelton

Keyword(s):

Microbial Community ◽

Dna Sequencing ◽

Environmental Dna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sediment Layer ◽

Biological Interactions ◽

Salt Flats ◽

Salt Crust ◽

Salt Pan

ABSTRACT We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio. This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape. IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.

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Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

Journal of the Asiatic Society of Bangladesh Science ◽

10.3329/jasbs.v41i1.46190 ◽

2015 ◽

Vol 41 (1) ◽

pp. 51-58

Author(s):

Mohammad Shamimul Alam ◽

Hawa Jahan ◽

Rowshan Ara Begum ◽

Reza M Shahjahan

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Fish Larva ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Valuable Insight ◽

Multiple Sequence ◽

Pcr Rflp ◽

Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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