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The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase-decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority (less than 1%) to the dominant bacterial group (54.0%) along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in "rare biosphere" might eventually become dominant in response to environmental change.

Microbial fuel cells (MFC) can effectively control the methane emissions from constructed wetland (CW). In this study, the effect of rhizosphere locations on the reduction of methane emission from CW by operating MFC was further studied. According to results, operating MFC in CW improved the COD removal and inhibited the methane emission from CW by 1/3. Plants (Cyperus alternifolius) roots at anode were more conducive to CW-MFC power generation. The highest power density (47.813 mW/m3) was observed in CW-MFC with rhizosphere at anode. The rhizosphere in cathode could improve CW-MFC COD removal. Operating MFC led to the competition between electrogens and methanogens, which changed the microbial community structure and biochemical processes in CW. Proteobacteria, as the main electricigen in CW-MFCs, were specifically enriched in CW-MFC with rhizosphere located in cathode. As the dominant archaea, methanobacteria and methanomicrobia were specifically enriched in CW-MFC with rhizosphere located in anode.

This paper aims to investigate the methane emissions from typical urban and rural constructed wetlands (CWs) associated with methanogen diversity using Illumina sequencing in microcosms from five different CWs planted with Cyperus alternifolius L. The results show that the average CH4 flux in summer in these five CWs was 0.33 gCH4 m−2 day−1, with a range of 0.01–1.52 g CH4 m−2 day−1 ((GWP: global warming potential) = 0.28–42.72 kg CO2eq m−2 year−1). Redundancy analysis (RDA) shows that methane fluxes were mostly impacted by local temperature (Ymethane = 4.66 Xtemp - 102.63, R2 = 0.81), which is considered to be a key environmental factor. The dissolved oxygen of all CWs showed a significantly negative correlation with CH4 emissions (R2 = −0.99, p = 0.01). Both the species richness index and species diversity index showed that Methanobacteria was the predominant class, with percentages ranging from 16.47% to 26.66% in the five CWs. The percentage of Methanomicrobia was 15.42–24.98% in the five CWs, and Methanococci was only found in the FengHuang constructed wetland. Other findings suggest that Methanomicrobiales in the Anlong Village constructed wetland was a dominant order and similar to a local paddy ecosystem in the Chengdu Plain.

High-saturation (40–100%), microbial gas hydrates have been acquired by expedition GMGS2 from the Taixinan Basin. In this study, geochemical and microbial features of hydrate-containing sediments from the drilling cores (GMGS2-09 and GMGS2-16) were characterized to explore their relationships with gas hydrate formation. Results showed that the average TOC content of GMGS2-09 and GMGS2-16 were 0.45% and 0.63%, respectively. They could meet the threshold for in situ gas hydrate formation, but were not available for the formation of high-saturation gas hydrates. The dominant members of Bacteria at the class taxonomic level were Alphaproteobacteria, Bacilli, Bacteroidia, Epsilonproteobacteria and Gammaproteobacteria, and those in Archaea were Marine_Benthic_Group_B (MBGB), Miscellaneous_Crenarchaeotic_Group (MCG), Group C3, Methanomicrobia and Methanobacteria. Indicators of microbes associated with thermogenic organic matter were measured. These include: (1) most of the dominant microbes had been found dominant in other gas hydrates bearing sediments, mud volcanos as well as oil/coal deposits; (2) hydrogenotrophic methanogens and an oilfield-origin thermophilic, methylotrophic methanogen were found dominant the methanogen community; (3) hydrocarbon-assimilating bacteria and other hyperthermophiles were frequently detected. Therefore, thermogenic signatures were inferred existed in the sediments. This deduction is consistent with the interpretation from the seismic reflection profiles. Owing to the inconsistency between low TOC content and gas hydrates with high saturation, secondary microbial methane generated from the bioconversion of thermogenic organic matters (oil or coal) was speculated to serve as enhanced gas flux for the formation of high-saturation gas hydrates. A preliminary formation model of high-saturation biogenic gas hydrates was proposed, in which diagenesis processes, tectonic movements and microbial activities were all emphasized regarding to their contribution to gas hydrates formation. In short, this research helps explain how microbial act and what kind of organic matter they use in forming biogenic gas hydrates with high saturations.

Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.

Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated ‘distance-decay’ patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.

Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of (13)CH4 and (13)CO2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

To investigate the community diversity and abundance of methanogens and their potential role in high arsenic groundwater, 17 groundwater samples from Hetao Plain of Inner Mongolia were investigated with an integrated method including 16S rRNA gene clone library, quantitative polymerase chain reaction and geochemistry analyses. Total arsenic (As Tot ) concentrations were 82.7–1088.7 μg/L and arsenite (AsIII) mostly dominated in these samples with percentages of 0.04–0.79. CH 4 concentrations ranged from 0.01 to 292 μg/L and distinctly elevated only when As Tot were relatively high and SO 4 2 − were distinctly low. Principal component analysis indicated that these samples were divided into three groups according to the variations of As Tot , CH 4 and SO 4 2 − . As Tot concentrations were distinctly high in the group with high CH 4 and low SO 4 2 − comparing to the other two groups (one with high CH 4 and high SO 4 2 − , the other with low CH 4 and SO 4 2 − ). The mcrA gene (methyl coenzyme-M reductase gene) based phylogenetic analysis of methanogens population showed that methanogenic archaea was diverse but mainly composed of Methanomicrobiales , Methanosarcinales , Methanobacteria and unidentified groups, with Methanomicrobiales being distinctly dominant (50.6%). The mcrA gene abundance in high arsenic groundwater ranged from 3.01 × 10 3 to 3.80 × 10 6 copies/L and accounted for 0–30.2% of total archaeal 16S rRNA genes. The abundance of mcrA genes was positively correlated with the concentrations of As Tot (R = 0.59), AsIII (R = 0.57) and FeII (R = 0.79), while it was negatively correlated with oxidation–reduction potential (R = − 0.66) and SO 4 2 − concentration (R = − 0.64). These results implied that methanogenic archaea might accelerate As release in groundwater aquifers in Hetao Plain.

This study investigated the possibilities of improving the biogasification from solid-state anaerobic digestion (SS-AD) of composting rice straw (RS) based on the optimized digestion temperature, initial substrate concentration (ISC) and C/N ratio. RS compounds, such as lignin, cellulose, and hemicellulose, were significantly degraded after composting. A significant interactive effect of temperature, ISC and C/N ratio was found on the biogasification of SS-AD of composting RS, and a maximum biogas production was achieved at 35.6°C, with a 20% ISC and a C/N ratio of 29.6:1. The verification experiment confirmed the optimization results. High-throughput sequencing analysis indicated that microbial communities in the SS-AD mainly consist of Methanobacteria, Bacteroidia, Clostridia, Betaproteobacteria, and Gammaproteobacteria. A dominant Methanobacteria was shifted from Methanobacterium to Methanoculleus during the SS-AD process. This study provides novel information about the interdependent effects and microbial behavior of AD.

The effects of lime mud from papermaking process (LMP) addition as buffer agent and inorganic nutrient on the anaerobic digestion stability of food waste (FW) were investigated under mesophilic conditions with the aim of avoiding volatile fatty acids accumulation, and inorganic elements deficiency. When LMP concentration ranged from 6.0 to 10g/L, the FW anaerobic digestion could maintain efficient and stable state. These advantages are attributed to the existence of Ca, Na, Mg, K, Fe, and alkaline substances that favor the methanogenic process. The highest CH4 yield of 272.8mL/g-VS was obtained at LMP and VS concentrations of 10.0 and 19.8g/L, respectively, with the corresponding lag-phase time of 3.84d and final pH of 8.4. The methanogens from residue digestates mainly consisted of Methanobrevibacter, coccus-type and sarcina-type methanogens with LMP addition compared to Methanobacteria in control. However, higher concentration of LMP inhibited methanogenic activities and methane production.

The performance of an up-flow anaerobic sludge blanket (UASB) reactor was investigated in the treatment of diluted pharmaceutical fermentation wastewater for a continuous operation of 140 days. The dynamics and compositions of the microbial community were monitored using polymerase chain reaction (PCR)-restriction fragment length polymorphism (PCR-RFLP) analysis. Increase of the organic loading rate (OLR) from 2.7 kg COD/m(3) d to 7.2 COD/m(3) d led to an increase in the COD removal efficiency from 83% to 91%. The dominant bacteria shifted from Proteobacteria (23.8%), Chloroflexi (14.5%) and Firmicutes (4.0%) to Firmicutes (48.4%), Bacteroidetes (9.5%) and Proteobacteria (5.4%). For archeaon, the dominant groups changed from Thermoplasmata (24.4%), Thermoprotei (18.0%) and Methanobacteria (30.8%) to Thermoplasmata (70.4%) and Methanomicrobia (16.8%). Firmicutes, Bacteroidetes, Thermoplasmata and Methanobacteria could outcompete other species and dominated in the reactor under higher OLR. The results indicated that, to some extent, microbial community shift could reflect the performance of the reactor and a significant community shift corresponded to a considerable process event.

We detected archaeal and bacterial glycerol dialkyl glycerol tetraether (GDGT) lipids in carbonate chimneys of the Lost City Hydrothermal Field, an alkaline system near the mid-Atlantic Ridge. Isoprenoidal, archaeal tetraethers from this site include “H-shaped” GDGTs, crenarchaeol and GDGTs with 0–3 cyclopentane moieties (here referred to as GDGTs 0–3). Concentrations of GDGT-3 do not track those of GDGTs 0–2 across the sample set, suggesting that its biosynthesis may be subject to different controls. Two branched, bacterial GDGTs (brGDGTs) common in terrigenous environments were also detected. Consulting previously published surveys of microbial diversity at Lost City and literature on known precursor-product relationships, we investigated the provenance of these GDGTs. The principal source of GDGTs 0–3 is likely ANME-1 archaea, abundant at Lost City. H-shaped GDGTs are likely derived from thermophilic Methanobacteria and Thermoprotei. Marine Group I Thaumarchaea detected in Lost City chimneys are a potential source of crenarchaeol, but it is unclear whether they are autotrophic nitrifiers or representatives of a hydrothermal ecotype with different physiology. The detection of branched GDGTs, possibly synthesized by Acidobacteria at Lost City, adds to a growing body of evidence that the capacity for their biosynthesis is not restricted to acidophilic soil bacteria and that they cannot strictly be considered indicators of terrigenous contributions to marine sediments. Input of hydrothermally derived lipids has the potential to complicate paleoproxy applications based on GDGTs. We propose that H-GDGTs be viewed as indicators of hydrothermal input and that their detection in sediments warrants caution in proxy application when a hydrothermal origin for co-occurring isoprenoidal and brGDGTs cannot be excluded.

Based on the successful performance of a lab-scale upflow anaerobic sludge blanket (UASB) reactor with the capacity of simultaneous methanogenesis and denitrification (SMD), the specific phylogenetic groups and community structure of microbes in the SMD granule in the UASB reactor were investigated by the construction of the Eubacteria and Archaea 16S rDNA clone libraries, fragment length polymorphism, and sequence blast. Real time quantitative-polymerase chain reaction (RTQ-PCR) technique was used to quantify the contents of Eubacteria and Archaea in the SMD granule. The contents of some special predominant methanogens were also investigated. The results indicated that the Methanosaeta and Methanobacteria were the predominant methanogens in all Archaea in the SMD granule, with contents of 71.59% and 22.73% in all 88 random Archaea clones, respectively. The diversity of Eubacteria was much more complex than that of Archaea. The low GC positive gram bacteria and epsilon-Protebacteria were the main predominant Eubacteria species in SMD granule, their contents were 49.62% and 12.03% in all 133 random Eubacteria clones respectively. The results of RTQ-PCR indicated that the content of Archaea was less than Eubacteria, the Archaea content in total microorganisms in SMD granule was about 27.6%.

In nature the biodegradation of xenobiotic compounds occurs through co-metabolism processes by microbial associations. The in vitro study of these metabolic processes entails the use of mixed microbial cultures, in which it is difficult to maintain degradative activity over time. We have set up appropriate working conditions to maintain, in methanogenic conditions, mixed cultures actively degrading bensulfuron-methyl. Initially the degrading activity of microbial cultures growing on two different media was comparable. Microscope observations of the mixed cultures revealed the presence of methanobacteria; moreover in medium MB it was found that the degradative activity of the mixture gradually diminished with time, the number of methanobacteria also diminishing and finally disappearing. On the contrary, in the M9 MOD medium the degradative activity remained stable.

Hassan Brim, Edward Lee, Scot Dowd, Adeyinka Laiyemo, Hassan Ashktorab Background: Linkage of specific bacterial markers to colorectal pathogenesis has been hampered by limited knowledge of the colonic microbiota and changing bacterial classification schemes. More than 80% of the colonic microbiota is not cultivatable and can only be assessed through metagenomic analysis. Aim: To perform a metagenomic analysis of 10 colon cancer tumors and their matched normal tissues. Methods: Metagenome sequencing was conducted on the illumina 2x150bp sequencing platform. Briefly DNA was prepared and libraries created using nextera library preparation kits. Sequencing was performed on each sample. For all samples an average of 20 million reads were obtained. Paired Sequencing reads were joined and entered into MG-RAST for metagenome analysis. The data was compared to M5NR using a maximum e-value of 1e-5, a minimum identity of 60 %, and a minimum alignment length of 15 measured in amino acids for protein databases. Results: Metagenomes were compared using best hit classification in two groups (normal and tumor). Based upon this best hit classification at the kingdom level in MG-RAST it was found, using one-way ANOVA, that tumor samples had a significantly higher classification related to Microviridae (bacteriophage) specifically related to Enterobacteria phage with a P= 0.0028. The other notable significant difference was the archaea. It was found at the class level that methanobacteria had higher classification hits in the normal samples (p = 0.03). Based upon functional gene abundance classification it was found that phage (P=0.007) as well as iron acquisition and metabolism genes (p= 0.05) were significantly different between the groups. Further analysis showed that as expected from the taxonomic classification data that tumor samples had higher levels of phage related functional classifications primarily related to phage capsid proteins. Other notable findings consisted of bacterial protein acetylation and deacetylation genes that were found to be significantly higher in normal tissue compared to tumor.