Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval

Methanogenic Community Characteristics and Its Influencing Factors in Reservoir Sediments on the Northeastern Qinghai Plateau

Reservoirs are a hotspot for methane emissions, a potent greenhouse gas. However, the microbial basis for methane production in the Qinghai Plateau reservoirs remains unclear. To explore the characteristics of methanogenic communities in reservoir sediments on the northeastern Qinghai Plateau, sediment samples were collected from 18 reservoirs in the Yellow River basin during May 2023 (dry season) and August 2023 (wet season). High-throughput sequencing technology was employed to analyze the community composition, diversity, and co-occurrence network of methanogens. Furthermore, FAPROTAX and Mantel analysis were used to assess the metabolic functions of methanogens and their influencing factors. The results showed that (1) the predominant genera of methanogens were Methanobacterium (28.87%) and Methanosarcina (21.67%). Hydrogenotrophic methanogenesis was the main pathway in the sediments. (2) Significant spatiotemporal differences were observed in the diversity of methanogenic communities (p < 0.05). The composition and diversity of these communities were found to be significantly influenced by temperature, pH, altitude, organic carbon, and total nitrogen (p < 0.05). (3) Methanosarcina, Methanobacterium, and Methanospirillum play crucial roles in maintaining the stability of methanogenic community networks. The co-occurrence network nodes are predominantly positively correlated (99.82%). These results provide data for further studies on carbon cycling in the Qinghai Plateau reservoirs.

Isolation of a methyl-reducing methanogen outside the Euryarchaeota

Methanogenic archaea are main contributors to methane emissions, and have a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades1-4, thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-euryarchaeal methanogens was lacking to corroborate their potential methanogenic ability and physiology. Here we report the isolation of a thermophilic archaeon LWZ-6 from an oil field. This archaeon belongs to the class Methanosuratincolia (originally affiliated with 'Candidatus Verstraetearchaeota') in the phylum Thermoproteota. Methanosuratincola petrocarbonis LWZ-6 is a strict hydrogen-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Methanosuratincolia members, strain LWZ-6 does not ferment sugars, peptides or amino acids. Its energy metabolism is linked only to methanogenesis, with methanol and monomethylamine as electron acceptors and hydrogen as an electron donor. Comparative (meta)genome analysis confirmed that hydrogen-dependent methylotrophic methanogenesis is a widespread trait among Methanosuratincolia. Our findings confirm that the diversity of methanogens expands beyond the classical Euryarchaeota and imply the importance of hydrogen-dependent methylotrophic methanogenesis in global methane emissions and carbon cycle.

Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest

Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 107 copies g-1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 105 and 104 copies g-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106 cells g-1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Impacts of Groundwater Pumping on Subterranean Microbial Communities in a Deep Aquifer Associated with an Accretionary Prism

Accretionary prisms are composed mainly of ancient marine sediment scraped from the subducting oceanic plate at convergent plate boundaries. Anoxic groundwater is stored in deep aquifers associated with accretionary prisms and can be collected via deep wells. We investigated how such groundwater pumping affects the microbial community in a deep aquifer. Groundwater samples were collected from a deep well drilled down to 1500 m every six months (five times in total) after completion of deep well construction and the start of groundwater pumping. Next-generation sequencing and clone-library analyses of 16S rRNA genes were used to describe the subterranean microbial communities in the samples. The archaea: the prokaryote ratio in groundwater increased significantly from 1 to 7% (0 and 7 months after initiating groundwater pumping) to 59 to 72% (13, 19, and 26 months after initiating groundwater pumping), and dominant prokaryotes changed from fermentative bacteria to sulfate-reducing archaea. The optimal growth temperature of the sulfate-reducing archaea, estimated based on the guanine-plus-cytosine contents of their 16S rRNA genes, was 48-52 °C, which agreed well with the groundwater temperature at the deep-well outflow. Our results indicated that, in deep aquifers, groundwater pumping enhances groundwater flow, and the supply of sulfate-containing seawater activates the metabolism of thermophilic sulfate-reducing archaea.

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

BACKGROUND

The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).

RESULTS

The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.

CONCLUSIONS

The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.

Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes

Lanzarote (Canary Islands, Spain) is one of the best terrestrial analogs to Martian volcanology. Particularly, Lanzarote lava tubes may offer access to recognizably preserved chemical and morphological biosignatures valuable for astrobiology. By combining microbiological, mineralogical, and organic geochemistry tools, an in-depth characterization of speleothems and associated microbial communities in lava tubes of Lanzarote is provided. The aim is to untangle the underlying factors influencing microbial colonization in Earth's subsurface to gain insight into the possibility of similar subsurface microbial habitats on Mars and to identify biosignatures preserved in lava tubes unequivocally. The microbial communities with relevant representativeness comprise chemoorganotrophic, halophiles, and/or halotolerant bacteria that have evolved as a result of the surrounding oceanic environmental conditions. Many of these bacteria have a fundamental role in reshaping cave deposits due to their carbonatogenic ability, leaving behind an organic record that can provide evidence of past or present life. Based on functional profiling, we infer that Crossiella is involved in fluorapatite precipitation via urea hydrolysis and propose its Ca-rich precipitates as compelling biosignatures valuable for astrobiology. In this sense, analytical pyrolysis, stable isotope analysis, and chemometrics were conducted to characterize the complex organic fraction preserved in the speleothems and find relationships among organic families, microbial taxa, and precipitated minerals. We relate organic compounds with subsurface microbial taxa, showing that organic families drive the microbiota of Lanzarote lava tubes. Our data indicate that bacterial communities are important contributors to biomarker records in volcanic-hosted speleothems. Within them, the lipid fraction primarily consists of low molecular weight n-alkanes, α-alkenes, and branched-alkenes, providing further evidence that microorganisms serve as the origin of organic matter in these formations. The ongoing research in Lanzarote's lava tubes will help develop protocols, routines, and predictive models that could provide guidance on choosing locations and methodologies for searching potential biosignatures on Mars.

The Potential of Digested Sludge-Assimilating Microflora for Biogas Production from Food Processing Wastes

Food processing wastes (FPWs) are residues generated in food manufacturing, and their composition varies depending on the type of food product being manufactured. Therefore, selecting and acclimatizing seed microflora during the initiation of biogas production is crucial for optimal outcomes. The present study examined the biogas production capabilities of digested sludge-assimilating and biogas-yielding soil (DABYS) and enteric (DABYE) microflorae when used as seed cultures for biogas production from FPWs. After subculturing and feeding these microbial seeds with various FPWs, we assessed their biogas-producing abilities. The subcultures produced biogas from many FPWs, except orange peel, suggesting that the heterogeneity of the bacterial members in the seed microflora facilitates quick adaptation to FPWs. Microflorae fed with animal-derived FPWs contained several methanogenic archaeal families and produced methane. In contrast, microflorae fed with vegetable-, fruit-, and crop-derived FPWs generated hydrogen, and methanogenic archaeal populations were diminished by repeated subculturing. The subcultured microflorae appear to hydrolyze carbohydrates and protein in FPWs using cellulase, pectinase, or protease. Despite needing enhancements in biogas yield for future industrial scale-up, the DABYS and DABYE microflorae demonstrate robust adaptability to various FPWs.

Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens

Methanothrix is widely distributed in natural and artificial anoxic environments and plays a major role in global methane emissions. It is one of only two genera that can form methane from acetate dismutation and through participation in direct interspecies electron transfer (DIET) with exoelectrogens. Although Methanothrix is a significant member of many methanogenic communities, little is known about its physiology. In this study, transcriptomics helped to identify potential routes of electron transfer during DIET between Geobacter metallireducens and Methanothrix thermoacetophila. Additions of magnetite to cultures significantly enhanced growth by acetoclastic methanogenesis and by DIET, while granular activated carbon (GAC) amendments impaired growth. Transcriptomics suggested that the OmaF-OmbF-OmcF porin complex and the octaheme outer membrane c-type cytochrome encoded by Gmet_0930, were important for electron transport across the outer membrane of G. metallireducens during DIET with Mx. thermoacetophila. Clear differences in the metabolism of Mx. thermoacetophila when grown via DIET or acetate dismutation were not apparent. However, genes coding for proteins involved in carbon fixation, the sheath fiber protein MspA, and a surface-associated quinoprotein, SqpA, were highly expressed in all conditions. Expression of gas vesicle genes was significantly lower in DIET- than acetate-grown cells, possibly to facilitate better contact between membrane-associated redox proteins during DIET. These studies reveal potential electron transfer mechanisms utilized by both Geobacter and Methanothrix during DIET and provide important insights into the physiology of Methanothrix in anoxic environments. IMPORTANCE Methanothrix is a significant methane producer in a variety of methanogenic environments including soils and sediments as well as anaerobic digesters. Its abundance in these anoxic environments has mostly been attributed to its high affinity for acetate and its ability to grow by acetoclastic methanogenesis. However, Methanothrix species can also generate methane by directly accepting electrons from exoelectrogenic bacteria through direct interspecies electron transfer (DIET). Methane production through DIET is likely to further increase their contribution to methane production in natural and artificial environments. Therefore, acquiring a better understanding of DIET with Methanothrix will help shed light on ways to (i) minimize microbial methane production in natural terrestrial environments and (ii) maximize biogas formation by anaerobic digesters treating waste.

Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

Methanobacterium alkalithermotolerans sp. nov., a novel alkaliphilic and hydrogen-utilizing methanogen isolated from an alkaline geothermal spring (La Crouen, New Caledonia)

An anaerobic, hydrogenotrophic methane-producing archaeon was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This methanogen, designated strain CAN^T, is alkaliphilic, thermotolerant, with Gram-positive staining non-motile cells. Strain CAN^T grows autotrophically using hydrogen exclusively as an energy source and carbon dioxide as the sole carbon source (without the requirement of yeast extract or other organic compounds). It grows at 20-45 °C (optimum, 45 °C) and pH 7.3-9.7 (optimum, pH 9.0). NaCl is not required for growth (optimum 0 %) but is tolerated up to 1.5 %. It resists novobiocin, streptomycin and vancomycin but is inhibited by ampicillin and penicillin, among other antibiotics. The genome consists of a circular chromosome (2.2 Mb) containing 2126 predicted protein-encoding genes with a G+C content of 36.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAN^T is a member of the genus Methanobacterium, most closely related to the alkaliphilic Methanobacterium alcaliphilum WeN4^T with 98.5 % 16S rRNA gene sequence identity. The genomes of strain CAN^T and M. alcaliphilum DSM 3459, sequenced in this study, share 71.6 % average nucleotide identity and 14.0 % digital DNA-DNA hybridization. Therefore, phylogenetic and physiological results indicate that strain CAN^T represents a novel species, for which the name Methanobacterium alkalithermotolerans sp. nov. is proposed, and strain CAN^T (=DSM 102889^T= JCM 31304^T) is assigned as the type strain.

Comparison of bacterial communities and their functional profiling using 16S rRNA gene sequencing between the inherent serpentine-associated sites, hyper-accumulator, downgradient agricultural farmlands, and distal non-serpentine soils

This study aims to determine and compare the bacterial community and functional profiles associated with serpentine sites, innate hyper-accumulating weed, downgradient agricultural farmlands and non-serpentine sites using 16S rRNA gene sequencing. Elemental analysis revealed that the serpentine rock and weathered soil have higher magnesium, nickel, chromium, magnesium/calcium and lower calcium/magnesium ratios and agricultural farmlands have recorded elevated chromium. Proteobacteria were found predominant, except the non-serpentine site which was rich in Cyanobacteria. PCA analysis at the genus level indicates the uniqueness of different experimental groups, except the hyperaccumulators which exhibited relatively less dissimilarity. The shift analysis showed the serpentine sites were characterized by the abundance of bacteria having heavy metal effluxion. The hyper-accumulating weeds were higher in plant growth-promoting bacteria expressing tolerance against heavy metals toxicity such as nickel, chromium, cobalt and arsenic. Besides, the agricultural lands were abundant in wetland-associated methanogens and metal (manganese, iron and zinc) transporting function related bacteria. The results suggest that the inherent edaphic factors including heavy metal content, the interacting behavior of hyperaccumulator's rhizosphere microbiota with soil and anthropogenic activities such as agricultural practices could be a major determinant of the variation in the bacterial community selection and abundance in the respective study sites.

Microflora communities which can convert digested sludge to biogas

In the present study, we developed several microflora communities that utilize digested sludge (DS), the recalcitrant waste product of anaerobic digestion, as a substrate for biogas production with the aim of their future application to DS recycling. Strict enrichment with DS as the sole nutrient source was introduced to culture microbes from soil and herbivore dung samples; microflora communities promoting stable levels of biogas production were obtained. The average methane and hydrogen yield from soil-derived microflora were 4.86 and 0.94 ml per 1.0 g DS, respectively. Notably, two microflora communities enriched from a riverbank sediment produced 20.79 ml and 14.10 ml methane from 1.0 g DS. By contrast, the methane and hydrogen yield for herbivore dung-derived microfloras were on average 1.31 ml and 1.87 ml per 1.0 g DS, respectively. Potent hydrogen-biogas producers were obtained from rabbit (4.12 ml per 1.0 g DS), goat (3.16 ml per 1.0 g DS), and sheep dung (2.52 ml per 1.0 g DS). The cultured microflora communities included representatives from the eubacterial genera, Clostridiaceae and Eubacteriaceae together with several anaerobic genera. Pseudomonas spp. are found in the riverbank sediment-derived microfloras, suggesting that the floras employ syntrophic acetate oxidation and hydrogentrophic methanogenesis (SAO-HM) pathway for methane production. The methanogenic microflora communities were dominated by bacteria from the Methanobacteriaceae family and unclassified archaea. Moreover, ascomycetous fungi and protists were found, implying that they act as oxygen scavengers and bacterial grazers, respectively. Enzymatic analysis suggested that the microfloras hydrolyze DS via cellulase, chitinase, and protease activities.

Effect of formic acid inflow on microbial properties of the anaerobic granular sludge in a UASB reactor

In the production of natural rubber, formate or acetate is added to the latex solution to coagulate the rubber; therefore, the wastewater contains high concentrations of organic acids, requiring the application of anaerobic treatment technology. In this study, a two-phase continuous flow experiment using a laboratory-scale upflow anaerobic sludge blanket (UASB) was conducted to investigate the influence of formate inflow on the microbial and physical characteristics of the retained granular sludge. In phase 1, acetate-based wastewater was used as feed, while in phase 2, formate-based wastewater was used as feed. In phase 1, the UASB exhibited high COD removal efficiency (97.2%); in addition, the retained sludge showed increased methane production from acetate and proliferation of acetate-utilizing Methanosaeta species. In phase 2, the UASB performed as well as phase 1, with 98.2% COD removal efficiency. Microbial community structure analysis confirmed that relatives of Methanobacterium formicicum present in the retained sludge were responsible for the degradation of formate in phase 2. However, decreased diameter and slight deterioration of granular sludge settleability were observed. In conclusion, formate inflow has low risk of interference with the process performance of the UASB, but it has negative effects on the physical properties of the granular sludge.

Performance and microbial community evaluation of full-scale two-phase anaerobic digestion of waste activated sludge

"Temperature Staging and Biological Phasing" (TSBP) is an improved two-phase anaerobic digestion (AD) technology. This technology hydrolyzes waste activated sludge (WAS) at 45 °C and converts methane at mesophilic temperature (35-38 °C), with hydraulic retention times of 3-5 d and 14-17 d, respectively. In this study, the performance and microbial community dynamics of full-scale TSBP-based sludge anaerobic digestion system were studied, and the technology was evaluated by energy balance and ecological benefit analysis. The stable operation for 390 d showed that the cumulative biogas yield was about 349,041 m³, the maximum biogas yield rate was 563.68 L/kg VS, and the VS degradation rate of organic matters in the sludge was 47.19%. Proteobacteria and Firmicutes were found to be the dominant bacteria in both thermophilic and mesophilic reactors. Methanobacterium and Methanosarcina were the two most abundant methanogenic genera in the AD samples. The aceticlastic methanogenesis was likely the predominant production pathway of methane in AD processes based on metagenomics. The TSBP system operated stably, and the recovered energy could achieve energy self-sufficiency, which provided technical reference for the anaerobic treatment of sludge.

Influence of oxygen on the vinyl acetate elimination pathway and microbial community structure of methanogenic sludge

Methanogenic-aerobic coupled processes were used to biological degradation of vinyl acetate (VA) to provide evidence of oxygen role for their complete elimination from different angles. First, physiological characterization of a continuous methanogenic-aerobic reactor fed by VA and glucose (G) showed that by adding G, the VA got 100% hydrolyzed to acetate, and then, by adding 1 mg·L^-1 ·d^-1 of dissolved oxygen (DO), this acetate got methanized by 40% and aerobically mineralized by 60%. Second, batch assays in the presence and absence of sodium azide suggest that VA at different concentrations was eliminated by both anaerobic and aerobic metabolic pathways, because without azide and in the presence of 1 mg DO·L^-1 increased methane and carbon dioxide formation rates at 80% and 75%, respectively. Finally, microbial population dynamics analysis of the reactor by DGGE-sequencing highlighted that Brevibacillus agri (aerobic) and Methanosarcina barkeri (anaerobic) were identified as responsible for VA elimination by up to 98.6%. PRACTITIONER POINTS: Vinyl acetate is removed by simultaneous methanation and aerobic respiration. Methanosarcina barkeri and Brevibacillus agri removed up to 99% of vinyl acetate. DO and VA have a selective effect on the metabolism and population dynamics.

Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments

Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Black Soldier Fly Diet Impacts Soil Greenhouse Gas Emissions From Frass Applied as Fertilizer

Increased global production of animal-based protein results in high greenhouse gas (GHG) emissions and other adverse consequences for human and planetary health. Recently, commercial insect rearing has been claimed a more sustainable source of animal protein. However, this system also leaves residues called frass, which—depending on the insect diet—is rich in carbon (C) and nitrogen (N), and could thus be used as fertilizer in agriculture. The impact of this kind of fertilizer on soil GHG emissions is yet unknown. Therefore, we investigated the effect of black soldier fly (Hermetia illucens L.) frass derived from a carbohydrate (Carb-) or a protein (Prot-) based diet applied at two different application rates to an arable soil on C and N fluxes and microbial properties in a 40-day incubation experiment. CO2, N2O, NO, N2, CH4, water extractable organic C (WEOC), and inorganic N were continuously measured quantitatively. At the end of the incubation, microbial biomass (MB), stoichiometry, community composition, and abundance of functional genes were assessed. Along with a strong increase in WEOC and CO2, Carb-frass caused strong initial N2O emissions associated with high N and C availability. In contrast, Prot-frass showed lower CO2 emissions and N2O release, although soil nitrate levels were higher. At the end of incubation, MB was significantly increased, which was more pronounced following Carb-frass as compared to Prot-frass application, and at higher amendment rates. Fungal abundance increased most from both frass types with an even stronger response at higher application rates, whereas bacterial abundance rose following Carb-frass as compared to Prot-application. Abundance of functional genes related to ammonia-oxidizing bacteria and archaea were enhanced by high frass application but did not clearly differ between frass types. C use efficiency of microorganisms, as revealed by the metabolic quotient, was most strongly reduced in the high Prot-frass application rate. Overall, insect diet influenced available C and N in frass and thus affected mineralization dynamics, GHG emissions, and microbial growth. Overall, emissions were very high undermining the potential environmental benefit of insect based protein production and calling for more detailed analyses before frass is widely applied in agriculture.

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane

A method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was controlled by adjusting reaction temperature and urea concentration in the mixture. Then, the mixture was filtered through the MWCOM. The rRNA and hybridized probes collected on the MWCOM were recovered and quantified using spectrophotometer and fluorospectrometer, respectively. The method showed high accuracy in detecting specific microbial rRNA in a defined nucleic acid mixture. Furthermore, the method was capable of simultaneous detection and quantification of multiple target rRNAs in a sample with sensitivity up to a single-base mismatch. The SCOPE method was tested and benchmarked against the reverse transcription-quantitative PCR (RT-qPCR) for the quantification of Bacteria, Archaea and some key methanogens in anaerobic sludge samples. It was observed that the SCOPE method produced comparatively more reliable and coherent results. In this way, the SCOPE method allows a simple and rapid detection and quantification of target microbial rRNAs for environmental microbial population analysis without any need for enzymatic reactions. Importance Microorganisms play integral roles in the earth's ecosystem. Microbial population and their activities significantly affect the global nutrient cycles. Quantification of key microorganisms provides important information that is required to understand their roles in the environment. Sequence-based analysis of microbial population is a powerful tool, but it only provides information on relative abundance of microorganisms. Hence, the development of a simpler and quick method for the quantification of microorganisms is necessary. To address the shortcomings of a variety of molecular methods reported so far, we developed a simple, rapid, accurate and multiplexed microbial rRNA quantification method to evaluate the abundance of specific microbial population in complex ecosystems. The developed method demonstrated high specificity, reproducibility, and applicability to such samples. The method is useful for quantitative detection of particular microbial members in the environment.

Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors

The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.

Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia)

(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.

Performance of anaerobic sludge and the microbial social behaviors induced by quorum sensing in a UASB after a shock loading

To understand the microbial social behaviors regulated by acyl-homoserine lactones (AHLs) in the upflow anaerobic sludge blanket (UASB) during the restored process after a shock loading, the correlation analyses of AHLs and components of extracellular polymeric substances (EPS), AHLs genes and microbes, and AHLs and microbes were investigated. The results showed that the performance could be restored by regulating influent organic loading rate stage-by-stage. A variation in microbial community and endogenous AHLs was also found during the restoration process. It was found that C₁₄-HSL had improved the synthesis of protein in EPS and resulted in better aggregation of microbes. C₄-HSL, as well as C₈-HSL and 3-oxoC₁₄-HSL, could prompt the metabolism of acidogenic fermentation bacteria. While 3-oxoC₆-HSL was identified as the key signal molecule in enhancing methanogenesis. The present work advanced the understanding of microbial social behaviors and provided an attractive strategy for the restoration of anaerobic digestion after shock loadings.

Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation

The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.

Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of "Candidatus Desulfomonile Palmitatoxidans"

Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C_{16 : 0}) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between the Desulfomonile sp. in HP culture and the type strain Desulfomonile tiedjei strain DCB-1^T, we propose a novel species designated as "Candidatus Desulfomonile palmitatoxidans." This bacterium shares 94.3 and 93.6% 16S rRNA gene identity with Desulfomonile limimaris strain DCB-M^T and D. tiedjei strain DCB-1^T, respectively. Based on sequence abundance of Desulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species "Ca. Desulfomonile palmitatoxidans" most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture and D. tiedjei strain DCB-1^T with short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, nor D. tiedjei strain DCB-1^T degraded palmitate when incubated with Methanobacterium formicicum as a possible methanogenic syntrophic partner. Unlike D. tiedjei strain DCB-1^T, "Ca. Desulfomonile palmitatoxidans" lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genus Desulfomonile is proposed. Our study reveals an unrecognized LCFA degradation feature of the Desulfomonile genus.

Characterization of Microbial Diversity and Community Structure in Fermentation Pit Mud of Different Ages for Production of Strong-Aroma Baijiu

In the traditional fermentation process of strong-aroma Baijiu, a fermentation pit mud (FPM) provides many genera of microorganisms for fermentation. However, the functional microorganisms that have an important effect on the quality of Baijiu and their changes with the age of fermentation pit (FP) are poorly understood. Herein, the Roche 454 pyrosequencing technique and a phospholipid fatty-acid analysis were employed to reveal the structure and diversity of prokaryotic communities in FPM samples that have been aged for 5, 30, and 100 years. The results revealed an increase in total prokaryotic biomass with an FP age; however, Shannon’s diversity index decreased significantly (p < 0.01). These results suggested that a unique microbial community structure evolved with uninterrupted use of the FP. The number of functional microorganisms, which could produce the flavor compounds of strong-aroma Baijiu, increased with the FP age. Among them, Clostridium and Ruminococcaceae are microorganisms that directly produce caproic acid. The increase of their relative abundance in the FPM might have improved the quality of strong-aroma Baijiu. Syntrophomonas, Methanobacterium, and Methanocorpusculum might also be beneficial to caproic acid production. They are not directly involved but provide possible environmental factors for caproic acid production. Overall, our study results indicated that an uninterrupted use of the FP shapes the particular microbial community structure in the FPM. This research provides scientific support for the concept that the aged FP yields a high-quality Baijiu.

Accelerated biomethane production from lignocellulosic biomass: Pretreated by mixed enzymes secreted by Trichoderma viride and Aspergillus sp

Biological pretreatment is a promising technology to increase biogas yield. The methane yield and microbial community resulting from anaerobic digestion of maize straw after pretreatment of enzymes [extracted from Trichoderma viride (ETv) and Aspergillus sp. (EAs)] at different mixing ratios [5/0, 4/1, 3/2, 2/3, 1/4, 0/5] were evaluated. The methane yields from mixed enzymes pretreatment were higher than single enzymes pretreatments of ETv and EAs. The optimal enzymes mixing ratio of ETv and EAs was found to be 2/3, with the cumulative methane yield 512.64 mL/g TS_added, which was 31.74% higher than the control. Enzymatic pretreatment promoted an increase in the abundance of bacteria and archaea associated with cellulose decomposition. The majority of bacteria and archaea were assigned to Bacteroidetes, Firmicutes and Methanosaeta.

Mercury methylation in rice paddy and accumulation in rice plant: A review

The bioavailability and toxicity of mercury (Hg) are dependent on its chemical speciation, in which methylmercury (MeHg) is the most toxic compound. Inorganic Hg can be transformed into MeHg in anaerobic conditions. Subsequent accumulation and biomagnification in the food chain pose a potential threat to human health. Previous studies have confirmed that paddy soil is an important site for MeHg production, and rice fields are an important source of MeHg in terrestrial ecosystems. Rice (Oryza sativa L.) is recently confirmed as a potential bioaccumulator plant of MeHg. Understanding the behaviour of Hg in rice paddies is important, particularly the mechanisms involved in Hg sources, uptake, toxicity, detoxification, and accumulation in crops. This review highlights the issue of MeHg-contaminated rice, and presents the current understanding of the Hg cycling in the rice paddy ecosystem, including the mechanism and processes of Hg species accumulation in rice plants and Hg methylation/demethylation processes in rice paddies and the primary controlling factors. The review also identified various research gaps in previous studies and proposes future research objectives to reduce the impact of Hg-contamination in rice crops.

Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater.

The Potential for CH4 Production by Syntrophic Microbial Communities in Diverse Deep Aquifers Associated with an Accretionary Prism and its Overlying Sedimentary Layers

Accretionary prisms are thick masses of sedimentary material scraped from the oceanic crust and piled up at convergent plate boundaries found across large regions of the world. Large amounts of anoxic groundwater and natural gas, mainly methane (CH₄), are contained in deep aquifers associated with these accretionary prisms. To identify the subsurface environments and potential for CH₄ production by the microbial communities in deep aquifers, we performed chemical and microbiological assays on groundwater and natural gas derived from deep aquifers associated with an accretionary prism and its overlying sedimentary layers. Physicochemical analyses of groundwater and natural gas suggested wide variations in the features of the six deep aquifers tested. On the other hand, a stable carbon isotope analysis of dissolved inorganic carbon in the groundwater and CH₄ in the natural gas showed that the deep aquifers contained CH₄ of biogenic or mixed biogenic and thermogenic origins. Live/dead staining of microbial cells contained in the groundwater revealed that the cell density of live microbial cells was in the order of 10⁴ to 10⁶‍ ‍cells‍ ‍mL^–1, and cell viability ranged between 7.5 and 38.9%. A DNA analysis and anoxic culture of microorganisms in the groundwater suggested a high potential for CH₄ production by a syntrophic consortium of hydrogen (H₂)-producing fermentative bacteria and H₂-utilizing methanogenic archaea. These results suggest that the biodegradation of organic matter in ancient sediments contributes to CH₄ production in the deep aquifers associated with this accretionary prism as well as its overlying sedimentary layers.

Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis

Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76^T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu²⁺ was used to lower bioavailable Cu²⁺ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10^-15 mol L^-1 free Cu²⁺ compared to standard conditions (10^-12 mol L^-1). This Cu²⁺ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10^-16 mol L^-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10^-12.7 mol L^-1), which also possesses a high amount of Cu-dependent enzymes.

DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea

Methylotrophic methanogenic archaea are an integral part of the carbon cycle in various anaerobic environments. Different from methylotrophic bacteria, methylotrophic methanogens assimilate both, the methyl compound and dissolved inorganic carbon. Here, we present DNA- and RNA-stable isotope probing (SIP) methods involving an effective labeling strategy using ¹³C-labeled dissolved inorganic carbon (DIC) as carbon source along with methanol as dissimilatory substrate.

Composition and ecology of bacterial and archaeal communities in anaerobic reactor fed with residual glycerol

Glycerol, the main residue of biodiesel production, can be used to produce organic acids and energy through anaerobic digestion. This study aimed to assess microbial structure, diversity, productivity, and stability and the influence of these parameters on the performance of an anaerobic reactor. The experimental setup consisted of an upflow anaerobic sludge blanket (UASB) reactor fed residual glycerol and nutrients. The organic loading rate (OLR) was gradually increased through five stages, and sludge samples were collected at each, followed by DNA extraction and PCR denaturing gradient gel electrophoresis (PCR-DGGE). The resulting bands were excised, amplified, and purified. The results showed increased bacterial diversity and richness from the inoculum (Rr 38.72 and H 2.32) and along stages I and II, reaching the highest populational parameters (Rr 194.06 and H 3.32). The following stages promote decreases in richness and diversity, achieving the lowest populational parameters on this study (Rr 11.53 and H 2.04). Biogas production increased along with functional organization due to the specialization of the bacterial community and a decrease in the methanogenic population, both promoted by the increase in OLR.

Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater

The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole. In contrast to other Fennoscandian deep biosphere communities studied to date, iron-oxidizing Gallionella dominated the bacterial communities, while methanogenic and ammonia-oxidizing archaea were the most prominent archaea, and a diverse fungal community was also detected. Potential for methane cycling and sulfate and nitrate reduction was confirmed by detection of the functional genes of these metabolic pathways. Organotrophs were less abundant, although carbohydrates were the most preferred of the tested substrates. The microbial communities shared features with those detected from other deep groundwaters with similar geochemistry, but the majority of taxa distinctive to Romuvaara are different from the taxa previously detected in saline deep groundwater in the Fennoscandian Shield, most likely because of the differences in water chemistry.

Isolation of known and potentially pathogenic tick-borne microorganisms from European ixodid ticks using tick cell lines

Ticks harbour and, in many cases transmit to their vertebrate hosts, a wide variety of pathogenic, apathogenic and endosymbiotic microorganisms. Recent molecular analyses have greatly increased the range of bacterial species potentially associated with ticks, but in most cases cannot distinguish between surface contaminants, microorganisms present in the remains of the previous blood meal and truly intracellular or tissue-associated bacteria. Here we demonstrate how tick cell lines, primary cell cultures and organ cultures can be used to isolate and propagate bacteria from within embryonic and adult Ixodes ricinus, Dermacentor marginatus and Dermacentor reticulatus ticks originating from different parts of Europe. We isolated and partially characterised four new strains of Spiroplasma from The Netherlands, Spain and Poland, two new strains of Rickettsia raoultii from Russia and Poland, one strain of Rickettsia slovaca from Spain and a species of Mycobacterium from the UK. Comparison with published sequences showed that the Spiroplasma strains were closely related to Spiroplasma ixodetis and the Mycobacterium isolate belonged to the Mycobacterium chelonae complex, while the R. raoultii and R. slovaca strains were similar to previously-validated species.

Effects of drought-stressed temperate forage legumes on the degradation and the rumen microbial community in vitro

According to climate change scenarios, central Europe may expect extending drought periods during summer. Lower water availability may influence the ruminal digestion of individual forage legume species differently. To test this hypothesis, Lotus corniculatus L. (var. Bull), Medicago lupulina L. (var. Ekola), Medicago falcata L. (wild seeds) and Trifolium repens L. (var. Rivendel) were each grown in parallel lots of control and drought-stressed monocultures. Rainout shelters (installed in May 2011 on a regrowth after first cut until harvest in mid of June) withheld rainfall of 40 mm in the drought stress treatment. Samples of dried (60°C) and milled (5 mm screen) forage legumes were incubated in a simulation experiment using Rusitec to assess drought effects on parameters for microbial metabolism. Degradability of dry matter and organic matter as well as methane production decreased in incubations with drought-stressed compared to control variants of legume species. Degradability of crude protein, neutral detergent fibre, acid detergent fibre and residual organic matter including non-fibre carbohydrates and lipids were affected by interactions between drought stress and species. Significant interactions were also found for ammonia concentrations, molar SCFA proportions and the microbial communities. It is concluded that drought stress for growing forage legumes influences their ruminal degradation and fermentation as well as the ruminal microbial communities of Bacteria and Archaea differently in a legume species-dependent manner.

Inhibition Studies with 2-Bromoethanesulfonate Reveal a Novel Syntrophic Relationship in Anaerobic Oleate Degradation

In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria.

Degradation of long-chain fatty acids (LCFAs) in methanogenic environments is a syntrophic process involving the activity of LCFA-degrading bacteria and hydrogen-utilizing methanogens. If methanogens are inhibited, other hydrogen scavengers are needed to achieve complete LCFA degradation. In this work, we developed two different oleate (C_18:1 LCFA)-degrading anaerobic enrichment cultures, one methanogenic (ME) and another in which methanogenesis was inhibited (IE). Inhibition of methanogens was attained by adding a solution of 2-bromoethanesulfonate (BrES), which turned out to consist of a mixture of BrES and isethionate. Approximately 5 times faster oleate degradation was accomplished by the IE culture compared with the ME culture. A bacterium closely related to Syntrophomonas zehnderi (99% 16S rRNA gene identity) was the main oleate degrader in both enrichments, in syntrophic relationship with hydrogenotrophic methanogens from the genera Methanobacterium and Methanoculleus (in ME culture) or with a bacterium closely related to Desulfovibrio aminophilus (in IE culture). A Desulfovibrio species was isolated, and its ability to utilize hydrogen was confirmed. This bacterium converted isethionate to acetate and sulfide, with or without hydrogen as electron donor. This bacterium also utilized BrES but only after 3 months of incubation. Our study shows that syntrophic oleate degradation can be coupled to desulfonation.

IMPORTANCE In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria.

Application of hybrid anaerobic reactor: Treatment of increasing cyanide containing effluents and microbial composition identification

The study endeavors the anaerobic treatment of cyanide-containing effluents using the hybrid anaerobic reactor, with self-immobilized granules under high up-flow velocities. Comparison of one-year time-course analyses of HARs treating high strength effluents containing cyanide and control indicates the importance of wastewater characteristics in development and maintenance of microbiome. Efforts were directed towards associating process performance with microbial dynamics. Presence of cyanide results in the accumulation of intermediates paralleled with a drop in abundance of sensitive aceticlastic methanogens. HAR appear to have better resilience than other identified digesters because of shielding effects and enhanced granule-wastewater contact. The predominance of Methanobacteriales in the presence of cyanide can be linked to its tolerance. It was found that methane yield is positively correlated with abundance of aceticlastic guilds (R = 0.830, CI = 0.01). Tolerant bacterial groups were also identified. The study advances our knowledge related to less energy intensive technology with the focus on the development of efficient HAR.

Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth

The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.

Biochar Modulates Methanogenesis through Electron Syntrophy of Microorganisms with Ethanol as a Substrate

Biochar has the potential to influence methanogenesis which is a key component of global carbon cycling. However, the mechanisms governing biochar's influence on methanogenesis is not well understood, especially its effects on interspecies relationships between methanogens and anaerobic bacteria (e.g., Geobacteraceae). To understand how different types of biochar influence methanogenesis, biochars derived from rice straw (RB), wood chips (WB), and manure (MB) were added to the methanogenic enrichment culture system of a paddy soil. Compared to the nonbiochar control, RB and MB additions accelerated methanogenesis remarkably, showing 10.7 and 12.3-folds higher methane production rate, respectively; while WB had little effect on methanogenesis. Using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electrochemical methods, RB and MB also had higher redox-active properties or charging and discharging capacities than WB, and the functional groups, mainly quinones, on the biochar surface played an important role in facilitating methanogenesis. Quantitative polymerase chain reaction results demonstrated that electronic syntrophy did exist between methanogens and Geobacteraceae. RB and MB stimulate methanogenesis by facilitating direct interspecies electron transfer between methanogens and Geobacteraceae. Our findings contribute to a better understanding of the effects of biochars from different feedstocks on methanogenesis and provide new evidence to the mechanisms of stimulating methanogenesis via biochar.

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique

The reduction of methane emissions by ruminants is a highly desirable goal to mitigate greenhouse gas emissions. Various feed additives have already been tested for their ability to decrease methane production; however, practical use is often limited due to negative effects on rumen fermentation or high costs. Organosulphur compounds from garlic (Allium sativum) and flavonoids have been identified as promising plant-derived compounds which are able to reduce methane production. Here, we evaluated the effects of a combination of garlic powder and bitter orange (Citrus aurantium) extracts, Mootral, on ruminal methane production, ruminal fermentation and the community of methanogenic Archaea by using the rumen simulation technique as ex vivo model. The experiment consisted of an equilibration period of 7 days, an experimental period of 8 days and a withdrawal period of 4 days. During the experimental period three fermenters each were either treated as controls (CON), received a low dose of Mootral (LD), a high dose of Mootral (HD), or monensin (MON) as positive control. Application of Mootral strongly reduced the proportion of methane in the fermentation gas and the production rate of methane. Moreover, the experimental mixture induced a dose-dependent increase in the production rate of short chain fatty acids and in the molar proportion of butyrate. Some effects persisted during the withdrawal period. Both, single strand conformation polymorphism and Illumina MiSeq 16S rRNA amplicon sequencing indicated an archaeal community distinct from CON and MON samples in the LD and HD samples. Among archaeal families the percentage of Methanobacteriaceae was reduced during application of both doses of Mootral. Moreover, several significant differences were observed on OTU level among treatment groups and after withdrawal of the additives for LD and HD group. At day 14, 4 OTUs were positively correlated with methane production. In conclusion this mixture of garlic and citrus compounds appears to effectively reduce methane production by alteration of the archaeal community without exhibiting negative side effects on rumen fermentation.

Isolation and characterization of a new Methanoculleus bourgensis strain KOR-2 from the rumen of Holstein steers

Objective

To isolate and identify new methanogens from the rumen of Holstein steers in Korea.

Methods

Representative rumen contents were obtained from three ruminally cannulated Holstein steers (793±8 kg). Pre-reduced media were used for the growth and isolation of methanogens. Optimum growth temperature, pH, and sodium chloride (NaCl) concentration as well as substrate utilization and antibiotic tolerance were investigated to determine the physiological characteristics of the isolated strain. Furthermore, the isolate was microscopically studied for its morphology. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification.

Results

One strain designated as KOR-2 was isolated and found to be a non-motile irregular coccus with a diameter of 0.2 to 0.5 μm. KOR-2 utilized H₂+CO₂ and formate but was unable to metabolize acetate, methanol, trimethylamine, 2-propanol, and isobutanol for growth and methane production. The optimum temperature and pH for the growth of KOR-2 were 38°C and 6.8 to 7.0, respectively, while the optimum NaCl concentration essential for KOR-2 growth was 1.0% (w/v). KOR-2 tolerated ampicillin, penicillin G, kanamycin, spectromycin, and tetracycline. In contrast, the cell growth was inhibited by chloramphenicol. Phylogenetic analysis of 16S rRNA and mcrA genes revealed the relatedness between KOR-2 and Methanoculleus bourgensis.

Conclusion

Based on the physiological and phylogenetic characteristics, KOR-2 was thought to be a new strain within the genus Methanoculleus and named Methanoculleus bourgensis KOR-2.

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing

AIMS

This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities.

METHODS AND RESULTS

The nontransgenic parental line was used as the control (Ck rice). DNA-based stable isotope probing (DNA-SIP) technology traced the rhizospheric active methanogens at the tillering stage. The results revealed significantly lower CH₄ emission flux from Bt soil than that from Ck soil during the whole growth period. The active methanogenic community composition remained stable. The RC-I lineage (77·9-79·8%) and Methanosaetaceae (13·9-15·1%) were the predominant active methanogens in Bt and Ck rice rhizospheres. However, the abundance of functionally active methanogens in the Bt rice rhizosphere was significantly reduced. Lower levels of root exudates (that included carbohydrate and organic acids) from Bt rice were also detected at the tillering stage.

CONCLUSION

This study found that the genetic modification of rice reduced the potential methanogenic substrates came from plant-derived root exudates, which represented an important factor in reducing CH₄ generation and active methanogenic archaeal abundance in Bt rhizosphere soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The effect of genetically modified (GM) insect-resistant crops on soil micro-organisms has become an issue of public concern, especially the indirect effect of plant metabolisms caused by the insertion of foreign genes. Methanogenesis, which is regarded as a critical ecological process in paddy soil, is influenced by plant root exudates; these are mainly derived from photosynthesis. The variations in root exudates across the Bt and Ck rice suggested the indirect influence of foreign gene insertion. DNA-SIP successfully traced the active methanogenic archaeal populations assimilating ¹³ C-labelled photosynthetic carbon and found a strong influence of planting Bt rice on active methanogens. As a consequence, we proposed that analysis of functionally active micro-organisms is more suitable for monitoring and predicting the environmental influence of GM plants.

Hydrogenotrophic Methanogenesis and Autotrophic Growth of Methanosarcina thermophila

Although Methanosarcinales are versatile concerning their methanogenic substrates, the ability of Methanosarcina thermophila to use carbon dioxide (CO2) for catabolic and anabolic metabolism was not proven until now. Here, we show that M. thermophila used CO2 to perform hydrogenotrophic methanogenesis in the presence as well as in the absence of methanol. During incubation with hydrogen, the methanogen utilized the substrates methanol and CO2 consecutively, resulting in a biphasic methane production. Growth exclusively from CO2 occurred slowly but reproducibly with concomitant production of biomass, verified by DNA quantification. Besides verification through multiple transfers into fresh medium, the identity of the culture was confirmed by 16s RNA sequencing, and the incorporation of carbon atoms from 13CO2 into 13CH4 molecules was measured to validate the obtained data. New insights into the physiology of M. thermophila can serve as reference for genomic analyses to link genes with metabolic features in uncultured organisms.

Geochemical and Microbiological Evidence for Microbial Methane Production in Deep Aquifers of the Cretaceous Accretionary Prism

Accretionary prisms are thick layers of sedimentary material piled up at convergent plate boundaries. Large amounts of anaerobic groundwater and methane (CH₄) are contained in the deep aquifers associated with accretionary prisms. In order to identify microbial activity and CH₄ production processes in the deep aquifers associated with the Cretaceous accretionary prism in Okinawa Island, Japan, we performed geochemical and microbiological studies using anaerobic groundwater and natural gas (mainly CH₄) samples collected through four deep wells. Chemical and stable hydrogen and oxygen isotope analyses of groundwater samples indicated that the groundwater samples obtained from each site originated from ancient seawater and a mixture of rainwater and seawater, respectively. Additionally, the chemical and stable carbon isotopic signatures of groundwater and natural gas samples suggested that CH₄ in the natural gas samples was of a biogenic origin or a mixture of biogenic and thermogenic origins. Microscopic observations and a 16S rRNA gene analysis targeting microbial communities in groundwater samples revealed the predominance of dihydrogen (H₂)-producing fermentative bacteria and H₂-utilizing methanogenic archaea. Moreover, anaerobic cultures using groundwater samples suggested a high potential for CH₄ production by a syntrophic consortium of H₂-producing fermentative bacteria and H₂-utilizing methanogenic archaea through the biodegradation of organic substrates. Collectively, our geochemical and microbiological data support the conclusion that the ongoing biodegradation of organic matter widely contributes to CH₄ production in the deep aquifers associated with the Cretaceous accretionary prism.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.