Variation in prokaryotic community composition as a function of resource availability in tidal creek sediments

Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench

The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO₂ reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO₂ reduction in both groups.

Calcium propionate supplementation alters the ruminal bacterial and archaeal communities in pre- and postweaning calves

The aim of this study was to determine the effect of calcium propionate (CaP) on rumen microbiota, fermentation indicators, and weight gain in calves both pre- and postweaning. Twenty-four newborn calves were randomly divided into 4 groups (2 × 2 factorial treatment arrangement): either pre- (90 d) or postweaning (160 d), and either without or with dietary CaP supplementation (5% dry matter). The CaP supplementation increased the body weight and rumen weight of the calves and lowered NH₃-N concentration in the rumen. Microbiota composition was characterized by sequencing the amplicons of the bacterial and archaeal 16S rRNA genes. The CaP supplementation decreased the relative abundance of the phylum Bacteroidetes but tended to increase that of Proteobacteria. In addition, CaP supplementation decreased the diversity of bacteria and archaea in the rumen compared with the calves fed the control diet. Linear discriminant analysis of the rumen microbiota revealed that Succinivibrionaceae and Methanobrevibacter were enriched in the CaP group postweaning. A correlation was also present between the acetate to propionate ratio and the species that acted as co-occurrence network hubs, including Succiniclasticum, Treponema, and Megasphaera. In conclusion, CaP supplementation can improve body weight gain and rumen growth and alter the ruminal microbiota in calves both pre- and postweaning.

Dynamics of bacterial community structure on intertidal sandflat inhabited by the ghost shrimp Nihonotrypaea harmandi (Decapoda: Axiidea: Callianassidae) in Tomioka Bay, Amakusa, Japan

Callianassid (ghost) shrimp has been claimed as an ecosystem engineer, as it is one of the most powerful bioturbating macrobenthos in intertidal sandflats. However, our knowledge about the relationship between areal distribution of bottom-dwelling ghost shrimps and dynamics of sediment microbial community structure remains obscured. We used automated ribosomal intergenic spacer analysis (ARISA) to reveal the bacterial community dynamics in the sediment of intertidal sandflat of Tomioka Bay, Kyushu, Japan, which is predominantly inhabited by a burrow-dwelling callianassid shrimp Nihonotrypaea harmandi. We found that the bacterial community structures of high and middle shrimp population areas were significantly differentiated from those of low population area (ANOSIM, R=0.10-0.18, p<0.01), while the former two areas were statistically indistinguishable (ANOSIM, R=-0.015, p>0.1). These results illustrated the potential importance of shrimp population density as a key factor in shaping the bacterial community structure and interpreting their dynamics in the sandflat. Furthermore, greater similarity between burrow and non-burrow communities was found in samples taken in autumn through winter than in those in summer (one-way ANOVA, p<0.05), whereas the phylotype richness was not simply differentiated by seasons. These results suggest not only that environmental variables including water temperature and salinity of the water column overlying the sandflat could exert notable impacts on the sediment bacterial community dynamics, but that the bio-irrigation and mixing by the ghost shrimp in permeable sandflat would strongly homogenize sediment particles, enhance solute transport surrounding the burrow and ambient subsurface substrate, and therefore reduce spatial differentiation of the bacterial community structure between the two sites. A comparison between present and previous studies of axiidean (former taxonomic group name, thalassinidean) ghost shrimps provides us with a comprehensive understanding of the shrimps' impacts on bacterial community dynamics, highlighting the importance of sediment permeability, a characteristic determined by the type of sediment, as a key controlling factor to shape spatial heterogeneity of bacterial community structure around burrow.

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 10⁶ copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 10⁶ copies per gram dry weight) was observed, but higher abundance (6.9 × 10⁶ to 1.02 × 10⁸ copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 10⁵ copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 10⁵ copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 10⁸ copies per gram dry weight) and pmoA gene (1.56 × 10⁷ copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.

Resource quantity affects benthic microbial community structure and growth efficiency in a temperate intertidal mudflat

Estuaries cover <1% of marine habitats, but the carbon dioxide (CO(2)) effluxes from these net heterotrophic systems contribute significantly to the global carbon cycle. Anthropogenic eutrophication of estuarine waterways increases the supply of labile substrates to the underlying sediments. How such changes affect the form and functioning of the resident microbial communities remains unclear. We employed a carbon-13 pulse-chase experiment to investigate how a temperate estuarine benthic microbial community at 6.5°C responded to additions of marine diatom-derived organic carbon equivalent to 4.16, 41.60 and 416.00 mmol C m(-2). The quantities of carbon mineralized and incorporated into bacterial biomass both increased significantly, albeit differentially, with resource supply. This resulted in bacterial growth efficiency increasing from 0.40 ± 0.02 to 0.55 ± 0.04 as substrates became more available. The proportions of diatom-derived carbon incorporated into individual microbial membrane fatty acids also varied with resource supply. Future increases in labile organic substrate supply have the potential to increase both the proportion of organic carbon being retained within the benthic compartment of estuaries and also the absolute quantity of CO(2) outgassing from these environments.

Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK)

We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and were 13.6% at 250 cm deep. Gene libraries for dsrA (dissimilatory sulfite reductase α-subunit) were constructed from the heavily contaminated (heavy metals) surface sediment (top 20 cm) and from the less contaminated and sulfate-depleted, deeper zone (250 cm). Certain cloned sequences were similar to dsrA found in members of the Syntrophobacteraceae, Desulfobacteraceae and Desulfovibrionaceae as well as a large fraction (60%) of novel sequences that formed a deep branching dsrA lineage. Phylogenetic analysis of metabolically active SRPs was performed by reverse transcription PCR and single strand conformational polymorphism analysis (RT-PCR-SSCP) of dsrA genes derived from extracted sediment RNA. Subsequent comparative sequence analysis of excised SSCP bands revealed a high transcriptional activity of dsrA belonging to Desulfovibrio species in the surface sediment. These results may suggest that members of the Desulfovibrionaceae are more active than other SRP groups in heavy metal-contaminated surface sediments.

Aceticlastic and NaCl-requiring methanogen "Methanosaeta pelagica" sp. nov., isolated from marine tidal flat sediment

Among methanogens, only 2 genera, Methanosaeta and Methanosarcina, are known to contribute to methanogenesis from acetate, and Methanosaeta is a specialist that uses acetate specifically. However, Methanosaeta strains so far have mainly been isolated from anaerobic digesters, despite the fact that it is widespread, not only in anaerobic methanogenic reactors and freshwater environments, but also in marine environments, based upon extensive 16S rRNA gene-cloning analyses. In this study, we isolated an aceticlastic methanogen, designated strain 03d30q(T), from a tidal flat sediment. Phylogenetic analyses based on 16S rRNA and mcrA genes revealed that the isolate belongs to the genus Methanosaeta. Unlike the other known Methanosaeta species, this isolate grows at Na(+) concentrations of 0.20 to 0.80 M, with an optimum concentration of 0.28 M. Quantitative estimation using real-time PCR detected the 16S rRNA gene of the genus Methanosaeta in the marine sediment, and relative abundance ranged from 3.9% to 11.8% of the total archaeal 16S rRNA genes. In addition, the number of Methanosaeta organisms increased with increasing depth and was much higher than that of Methanosarcina organisms, suggesting that aceticlastic methanogens contribute to acetate metabolism to a greater extent than previously thought in marine environments, where sulfate-reducing acetate oxidation prevails. This is the first report on marine Methanosaeta species, and based on phylogenetic and characteristic studies, the name "Methanosaeta pelagica" sp. nov. is proposed for this novel species, with type strain 03d30q.

A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan

Anaerobic methane-oxidizing archaea (ANME) are known to play an important role in methane flux, especially in marine sediments. The 16S rRNA genes of ANME have been detected in terrestrial freshwater subsurfaces. However, it is unclear whether ANME are actively involved in methane oxidation in these environments. To address this issue, Holocene sediments in the subsurface of the Kanto Plain in Japan were collected for biogeochemical and molecular analysis. The potential activity of the anaerobic oxidation of methane (AOM) (0.38-3.54 nmol cm⁻³ day⁻¹) was detected in sediment slurry incubation experiments with a (13) CH(4) tracer. Higher AOM activity was observed in low-salinity treatment compared with high-salinity condition (20‰), which supports the adaptation of ANME in freshwater habitats. The 16S rRNA sequence analysis clearly revealed the presence of a distinct subgroup of ANME-1, designated ANME-1a-FW. Phylogenetic analysis of the mcrA genes also implied the presence of the distinct subgroup in ANME-1. ANME-1a-FW was found to be the most dominant active group in the archaeal communities on the basis of 16S rRNA analysis (75.0-93.8% of total archaeal 16S rRNA clones). Sulfate-reducing bacteria previously known as the syntrophic bacterial partners of ANME-1 was not detected. Our results showed that ANME-1a-FW is adapted to freshwater habitats and is responsible for AOM in terrestrial freshwater subsurface environments.

Investigation and optimization of a passively operated compost-based system for remediation of acidic, highly iron- and sulfate-rich industrial waste water

A passively operated multi-stage bioremediation system utilizing composted agricultural waste products and an artificial wetland system was found to be effective for purification of acidic, iron- and sulfate-rich waste water derived from titanium mineral processing. The main microbial players involved in the remediation system processes and the dynamics were investigated; mineral processing waste water-filled sludge dams possessed stable microbial communities that included Acidithiobacillus, Desulfurella, and acidophilic, anaerobic fermenters of the order Bacteroidales. These groups were enriched in a subsequent potato waste-based iron mobilization pre-treatment stage. Within downstream reduction treatment stages ("reduction cells"), compost/straw decomposition and associated sulfur/sulfate and iron reduction were carried out by a complex mix of aerobic and anaerobic bacteria. The efficaciousness of the system without replacement of the compost was found to steadily decline following 2 years of operation and corresponded with the reduction cell communities becoming simultaneously more diverse and homogenous. Microcosm-based experiments demonstrated that operational declines were due to unsustained supply of suitable labile carbon sources combined with spatial heterogeneity within the layered design of the reduction stage of the system resulting in inadequate redox conditions. Temperature was not found to be a critical performance factor in the range of 10-25 degrees C. Application of a combined emulsified oil/molasses amendment was found to be highly effective in promoting a microbial community capable of remediating waste water with high iron and sulfate levels. Acidophilic members of the order Bacteroidales were found to be critical in the investigated remediation system, providing organic donors for subsequent metal and sulfur transformations and could have a broader ecological significance than previously suspected.