@article{lyu_rotaru_pimentel_zhang_rittmann_2022, title={Editorial: The methane moment - Cross-boundary significance of methanogens: Preface}, volume={13}, url={http://dx.doi.org/10.3389/fmicb.2022.1055494}, DOI={10.3389/fmicb.2022.1055494}, abstractNote={COPYRIGHT © 2022 Lyu, Rotaru, Pimentel, Zhang and Rittmann. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: The methane moment Cross-boundary significance of methanogens: Preface}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Lyu, Zhe and Rotaru, Amelia-Elena and Pimentel, Mark and Zhang, Cui-Jing and Rittmann, Simon K.-M. R.}, year={2022}, month={Nov} }
 @article{lyu_2021, title={Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production}, volume={66}, url={http://dx.doi.org/10.1007/s10620-021-06839-0}, DOI={10.1007/s10620-021-06839-0}, number={11}, journal={Digestive Diseases and Sciences}, publisher={Springer Science and Business Media LLC}, author={Lyu, Zhe}, year={2021}, month={Nov}, pages={3661–3664} }
 @article{akinyemi_shao_lyu_drake_liu_whitman_2021, title={Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis}, volume={10}, url={http://dx.doi.org/10.1021/acssynbio.1c00322}, DOI={10.1021/acssynbio.1c00322}, abstractNote={Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO2 to CH4. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.}, number={11}, journal={ACS Synthetic Biology}, publisher={American Chemical Society (ACS)}, author={Akinyemi, Taiwo S. and Shao, Nana and Lyu, Zhe and Drake, Ian J. and Liu, Yuchen and Whitman, William B.}, year={2021}, month={Nov}, pages={3028–3039} }
 @article{zhang_cotter_lyu_shimkets_igoshin_2020, title={Data-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial Aggregation}, volume={5}, url={https://doi.org/10.1128/mSystems.00518-20}, DOI={10.1128/mSystems.00518-20}, abstractNote={
            Self-organization into spatial patterns is evident in many multicellular phenomena. Even for the best-studied systems, our ability to dissect the mechanisms driving coordinated cell movement is limited. While genetic approaches can identify mutations perturbing multicellular patterns, the diverse nature of the signaling cues coupled to significant heterogeneity of individual cell behavior impedes our ability to mechanistically connect genes with phenotype. Small differences in the behaviors of mutant strains could be irrelevant or could sometimes lead to large differences in the emergent patterns. Here, we investigate rescue of multicellular aggregation in two mutant strains of
            Myxococcus xanthus
            mixed with wild-type cells. The results demonstrate how careful quantification of cell behavior coupled to data-driven modeling can identify specific motility features responsible for cell aggregation and thereby reveal important synergies and compensatory mechanisms. Notably, mutant cells do not need to precisely recreate wild-type behaviors to achieve complete aggregation.
          }, number={4}, journal={mSystems}, publisher={American Society for Microbiology}, author={Zhang, Zhaoyang and Cotter, Christopher R. and Lyu, Zhe and Shimkets, Lawrence J. and Igoshin, Oleg A.}, editor={Rust, MichaelEditor}, year={2020}, month={Aug} }
 @article{zhang_cotter_lyu_shimkets_igoshin_2020, title={Data-driven models reveal mutant cell behaviors important for myxobacterial aggregation}, volume={2}, url={http://dx.doi.org/10.1101/2020.02.08.939462}, DOI={10.1101/2020.02.08.939462}, abstractNote={Abstract}, journal={[]}, publisher={Cold Spring Harbor Laboratory}, author={Zhang, Zhaoyang and Cotter, Christopher R. and Lyu, Zhe and Shimkets, Lawrence J. and Igoshin, Oleg A.}, year={2020}, month={Feb} }
 @article{lyu_shao_chou_shi_patel_duin_whitman_2020, title={Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis}, volume={202}, DOI={10.1128/jb.00654-19}, abstractNote={
            Mcr is the key enzyme in methanogenesis and a promising candidate for bioengineering the conversion of methane to liquid fuel. Our knowledge of Mcr is still limited. In terms of complexity, uniqueness, and environmental importance, Mcr is more comparable to photosynthetic reaction centers than conventional enzymes. PTMs have long been hypothesized to play key roles in modulating Mcr activity. Here, we directly link the
            mmpX
            gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights into its substrate specificity and putative cofactor binding sites. This is also the first time that a PTM of McrA has been shown to have a substantial impact on both methanogenesis and growth in the absence of additional stressors.
          }, number={3}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Lyu, Zhe and Shao, Nana and Chou, Chau-Wen and Shi, Hao and Patel, Ricky and Duin, Evert C. and Whitman, William B.}, editor={Becker, AnkeEditor}, year={2020}, month={Jan} }
 @article{lyu_liu_2019, title={Diversity and Taxonomy of Methanogens}, DOI={10.1007/978-3-319-78108-2_5}, journal={Biogenesis of Hydrocarbons}, publisher={Springer International Publishing}, author={Lyu, Zhe and Liu, Yuchen}, year={2019}, month={Jul}, pages={19–77} }
 @article{zhao_lyu_long_akinyemi_manakongtreecheep_söll_whitman_vinyard_liu_2019, title={The Nbp35/ApbC homolog acts as a nonessential [4Fe‐4S] transfer protein in methanogenic archaea}, volume={594}, DOI={10.1002/1873-3468.13673}, abstractNote={The nucleotide binding protein 35 (Nbp35)/cytosolic Fe‐S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe‐S cluster assembly scaffold required for the maturation of Fe‐S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe‐S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe‐4S] cluster that can be transferred to a [4Fe‐4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe‐4S] cluster transfer protein in methanogenic archaea.}, number={5}, journal={FEBS Letters}, publisher={Wiley}, author={Zhao, Cuiping and Lyu, Zhe and Long, Feng and Akinyemi, Taiwo and Manakongtreecheep, Kasidet and Söll, Dieter and Whitman, William B. and Vinyard, David J. and Liu, Yuchen}, year={2019}, month={Nov}, pages={924–932} }
 @article{lyu_whitman_2019, title={Transplanting the pathway engineering toolbox to methanogens}, volume={59}, DOI={10.1016/j.copbio.2019.02.009}, abstractNote={Biological methanogenesis evolved early in Earth's history and was likely already a major process by 3.5 Ga. Modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts. Owing to their long evolution and extensive adaptations to various habitats, methanogens possess enormous metabolic and physiological diversity. Not only does this diversity offers unique opportunities for biotechnology applications, but also reveals their direct impact on the environment, agriculture, and human and animal health. These efforts are facilitated by an advanced genetic toolbox, emerging new molecular tools, and systems-level modelling for methanogens. Further developments and convergence of these technical advancements provide new opportunities for bioengineering methanogens.}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={Lyu, Zhe and Whitman, William B}, year={2019}, month={Oct}, pages={46–54} }
 @article{lyu_chou_shi_wang_ghebreab_phillips_yan_duin_whitman_2018, title={Assembly of Methyl Coenzyme M Reductase in the Methanogenic Archaeon Methanococcus maripaludis}, volume={200}, url={https://doi.org/10.1128/JB.00746-17}, DOI={10.1128/JB.00746-17}, abstractNote={ABSTRACT}, number={7}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Lyu, Zhe and Chou, Chau-Wen and Shi, Hao and Wang, Liangliang and Ghebreab, Robel and Phillips, Dennis and Yan, Yajun and Duin, Evert C. and Whitman, William B.}, editor={Metcalf, William W.Editor}, year={2018}, month={Apr} }
 @article{lyu_liu_2018, title={Diversity and Taxonomy of Methanogens}, DOI={10.1007/978-3-319-53114-4_5-2}, journal={Biogenesis of Hydrocarbons}, publisher={Springer International Publishing}, author={Lyu, Zhe and Liu, Yuchen}, year={2018}, pages={1–59} }
 @article{lyu_lu_2018, title={Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments}, url={https://doi.org/10.1038/ismej.2017.173}, DOI={10.1038/ismej.2017.173}, abstractNote={Abstract}, journal={The ISME Journal}, author={Lyu, Zhe and Lu, Yahai}, year={2018}, month={Feb} }
 @article{lyu_shao_akinyemi_whitman_2018, title={Methanogenesis}, volume={28}, DOI={10.1016/j.cub.2018.05.021}, abstractNote={Methanogenesis is an anaerobic respiration that generates methane as the final product of metabolism. In aerobic respiration, organic matter such as glucose is oxidized to CO2, and O2 is reduced to H2O. In contrast, during hydrogenotrophic methanogenesis, H2 is oxidized to H+, and CO2 is reduced to CH4. Although similar in principle to other types of respiration, methanogenesis has some distinctive features: the energy yield is very low, ≤1 ATP per methane generated, and only methanogens - organisms capable of this specialized metabolism - carry out biological methane production. Methanogens, like the process they catalyze, are similarly distinctive. Methanogens are comprised exclusively of archaea. They are obligate methane producers, that is, they do not grow using fermentation or alternative electron acceptors for respiration. Finally, methanogens are strict anaerobes and do not grow in the presence of O2. Historically, methanogenesis has been viewed as a highly specialized metabolism restricted to a narrow group of prokaryotes. However, recent developments have revealed enormous diversity within the methanogens and suggest that this metabolism is one of the most ancient on earth.}, number={13}, journal={Current Biology}, publisher={Elsevier BV}, author={Lyu, Zhe and Shao, Nana and Akinyemi, Taiwo and Whitman, William B.}, year={2018}, month={Jul}, pages={R727–R732} }
 @article{lyu_li_he_zhang_2017, title={An Important Role for Purifying Selection in Archaeal Genome Evolution}, volume={2}, url={https://doi.org/10.1128/mSystems.00112-17}, DOI={10.1128/msystems.00112-17}, abstractNote={The evolution of genome complexities is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis of genetic drift, which showed relaxed purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes.}, number={5}, journal={mSystems}, publisher={American Society for Microbiology}, author={Lyu, Zhe and Li, Zhi-Gang and He, Fei and Zhang, Ziding}, editor={Rust, MichaelEditor}, year={2017}, month={Oct}, pages={e00112–17} }
 @article{lyu_chou_shi_patel_duin_whitman_2017, title={Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase}, volume={10}, url={https://doi.org/10.1101/211441}, DOI={10.1101/211441}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Lyu, Zhe and Chou, Chau-wen and Shi, Hao and Patel, Ricky and Duin, Evert C. and Whitman, William B.}, year={2017}, month={Oct} }
 @article{pikuta_lyu_williams_patel_liu_hoover_busse_lawson_whitman_2017, title={Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions for the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S.soli and S. suarezii.}, url={http://europepmc.org/abstract/med/28150571}, DOI={10.1099/ijsem.0.001838}, abstractNote={A novel psychrotolerant bacterium, strain ISLP-3T, was isolated from a sample of naturally formed ice sculpture on the shore of Lake Podprudnoye in Antarctica. Cells were motile, stained Gram-positive, non-spore-forming, straight or slightly curved rods with the shape of a baseball bat. The new isolate was facultatively anaerobic and catalase-positive. Growth occurred at 3-35 °C with an optimum at 22-24 °C, 0-2 % (w/v) NaCl with an optimum at 0.3 % and pH 6.2-9.5 with an optimum at pH 7.5. Strain ISLP-3T grew on several carbon sources, with the best growth on cellobiose. The isolate possessed ureolytic activity but growth was inhibited by urea. The strain was sensitive to: ampicillin, gentamycin, kanamycin rifampicin, tetracycline and chloramphenicol. Major fatty acids were: anteiso-C15 : 0, iso-C16 : 0, C16 : 0, C14 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H4). The genomic G+C content was 69.5 mol%. The 16S rRNA gene showed 99 % sequence similarity to that of Sanguibacter suarezii ST-26T, but their recA genes shared ≤91 % sequence similarity, suggesting that this new isolate represents a novel species within the genus Sanguibacter. This conclusion was supported by average nucleotide identity, which was ≤91 % to the most closely related strain. The name Sanguibacter gelidistatuariae sp. nov. is proposed for the novel species with the type strain ISLP-3T=ATCC TSD-17T=DSM 100501T=JCM 30887T). The complete genome draft sequence of ISLP-3T was deposited under IMG OID 2657245272. Emendments to the descriptions of related taxa have been made based on experimental data from our comparative analysis.}, journal={International journal of systematic and evolutionary microbiology}, author={Pikuta, E.V. and Lyu, Z. and Williams, M.D. and Patel, N.B. and Liu, Y. and Hoover, R.B. and Busse, H.J. and Lawson, P.A. and Whitman, W.B.}, year={2017}, month={Feb} }
 @article{williamwhitmania taraxaci gen. nov., sp. nov., a proteolytic anaerobe with a novel type of cytology from lake untersee in antarctica, description of williamwhitmaniaceae fam. nov., and emendation of the order bacteroidales krieg 2012._2017, volume={9}, url={http://europepmc.org/abstract/med/28905708}, DOI={10.1099/ijsem.0.002266}, abstractNote={The proteolytic bacterium strain A7P-90mT was isolated from Lake Untersee, Antarctica. The anoxic water was collected from a perennially sealed (~100 millennia) glacial ice lake. Gram-stain-negative cells were 0.18-0.3×8.0-25.0 µm in size, straight, slender rods with unusual gliding motility by external, not previously reported, organelles named here as antiae. At the end of stationary phase of growth, spheroplasts were terminally formed and the cells resembled dandelions. After death, cells were helical. The isolate was an athalassic, strictly anaerobic and catalase-negative proteolytic chemoorganotroph. It was moderately psychrophilic with a temperature range for growth of 3-26 °C and an optimum at 22-23 °C. The pH range for growth was 5.5-7.8 with an optimum at 6.9. Major cellular fatty acids were branched pentadecanoic and tridecanoic acids, and saturated tetradecanoic acids. The quinone system comprised menaquinone MK-7. The strain was sensitive to all checked antibiotics and ascorbic acid. The G+C content of the genomic DNA was 42.6 mol%. Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order Bacteroidales and formed a novel family with the proposed name Williamwhitmaniaceae fam. nov. The description of the order Bacteroidales was emended accordingly. The name Williamwhitmania taraxaci gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain A7P-90mT (=DSM 100563T=JCM 30888T). The complete draft genome sequence was deposited at the Joint Genomes Institute (JGI) under number IMG OID 2654588148 and in SRA listed as SRP088197.}, journal={International journal of systematic and evolutionary microbiology}, year={2017}, month={Sep} }
 @article{lyu_jain_smith_fetchko_yan_whitman_2016, title={Engineering the Autotroph Methanococcus maripaludis for Geraniol Production.}, url={http://europepmc.org/abstract/med/26886063}, journal={ACS synthetic biology}, author={Lyu, Z and Jain, R and Smith, P and Fetchko, T and Yan, Y and Whitman, WB}, year={2016}, month={Feb} }
 @article{lyu_whitman_2016, title={Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease.}, url={http://europepmc.org/abstract/med/27261368}, publisher={CMLS}, author={Lyu, Z and Whitman, WB}, year={2016}, month={Jun} }
 @article{pikuta_menes_bruce_lyu_patel_liu_hoover_busse_lawson_whitman_2016, title={Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere.}, volume={66}, url={http://europepmc.org/abstract/med/27902285}, DOI={10.1099/ijsem.0.001552}, abstractNote={A Gram-stain-positive bacterium, strain LZ-22T, was isolated from a rhizosphere of moss Leptobryum sp. collected at the shore of Lake Zub in Antarctica. Cells were motile, straight or pleomorphic rods with sizes of 0.6-1.0×3.5-10 µm. The novel isolate was a facultatively anaerobic, catalase-positive, psychrotolerant mesophile. Growth was observed at 3-41 °C (optimum 24-28 °C), with 0-7 % (w/v) NaCl (optimum 0.25 %) and at pH 4.0-9.0 (optimum pH 7.8). The quinone system of strain LZ-22T possessed predominately menaquinone MK-9(H4). The genomic G+C content was 70.2 mol%. Strain 10J was isolated from a biofilm of sediment microbial fuel cell, in Uruguay and had 99 % 16S rRNA gene sequence similarity to strain LZ-22T. DNA-DNA-hybridization values of 84 % confirmed that both strains belonged to the same species. Both strains grew on sugars, proteinaceous compounds, and some amino- and organic acids. Strain LZ-22T uniquely grew on D-enantiomers of histidine and valine while neglecting growth on L-enantiomers. Both strains were sensitive to most of the tested antibiotics but resistant to tested nitrofurans and sulfanilamides. Phylogenetic analyses of the 16S rRNA gene sequences indicated that the strains were related to members of the family Propionibacteriaceae (~93-94 % 16S rRNA gene sequence similarity) with formation of a separate branch within the radiation of the genera Granulicoccus and Luteococcus. Based on phenotypic and genotypic characteristics, we propose the affiliation of both strains into a novel species of a new genus. The name Raineyella antarctica gen. nov., sp. nov. is proposed for the novel taxon with the type strain LZ-22T (=ATCC TSD-18T=DSM 100494T=JCM 30886T).}, number={12}, journal={International journal of systematic and evolutionary microbiology}, author={Pikuta, EV and Menes, RJ and Bruce, AM and Lyu, Z and Patel, NB and Liu, Y and Hoover, RB and Busse, HJ and Lawson, PA and Whitman, WB}, year={2016}, month={Dec}, pages={5529–5536,} }
 @article{lyu_lu_2015, title={Comparative genomics of three Methanocellales strains reveal novel taxonomic and metabolic features}, volume={2}, url={https://doi.org/10.1111/1758-2229.12283}, DOI={10.1111/1758-2229.12283}, abstractNote={Summary}, journal={Environmental Microbiology Reports}, publisher={Wiley-Blackwell}, author={Lyu, Zhe and Lu, Yahai}, year={2015}, month={Feb}, pages={n/a-n/a} }
 @inproceedings{pikuta_lyu_whitman_labrake_wallis_wickramarathne_wickramasinghe_hoover_2015, title={Microbiological investigation of two chondrite meteorites: Murchison and Polonnaruwa}, DOI={10.1117/12.2191203}, abstractNote={The question of the contamination of meteorites by modern environmental microorganisms is an issue that has been raised since evidence for biological remains in carbonaceous meteorites was first published in the early 1960's.1-3 The contamination hypothesis has been raised for recent fossils of diatoms and filamentous cyanobacteria found embedded in the stones even though the nitrogen content of the fossils was below the 0.5% detection limit for Energy Dispersive X-ray Spectroscopy (EDS) of the Field Emission Scanning Electron Microscope. All modern biological contaminants should have nitrogen content in the detectable range of 2% to 20% indicating the remains are ancient fossils rather than living or Holocene cells. In our work, the possibility that extremophilic bacteria from our lab collection might be able to metabolize organic matter in the studied meteorites was tested. The potential toxic or inhibitory growth effects were also checked for different anaerobic cultures. UV exposed meteorite samples with consequent sterile extraction of the internal part were subjected to anaerobic cultivation techniques. As a result, eight anaerobic strains were isolated from internal and exterior parts of the studied meteorites. Preliminary results of their morphology, cytology, physiology, and molecular (16SrRNA sequencing) studies are presented and discussed in this article.}, booktitle={Instruments, Methods, and Missions for Astrobiology XVII}, publisher={SPIE-Intl Soc Optical Eng}, author={Pikuta, Elena V. and Lyu, Zhe and Whitman, William B. and LaBrake, Geneviev R. and Wallis, Jamie and Wickramarathne, Keerthi and Wickramasinghe, N. Chandra and Hoover, Richard B.}, editor={Hoover, Richard B. and Levin, Gilbert V. and Rozanov, Alexei Yu. and Wickramasinghe, Nalin C.Editors}, year={2015}, month={Sep} }
 @inproceedings{lyu_pikuta_hagel_labrake_hoover_whitman_2015, title={Molecular studies of anaerobic strains from Antarctica and their taxonomic identifications}, DOI={10.1117/12.2192787}, abstractNote={We present phylogenetic analyses for four anaerobic bacterial isolates from samples collected in the Schirmacher Oasis and Lake Untersee in Antarctica. Near-full length of 16S rRNA genes were amplified from the four strains and sequenced for identification of their close relatives and their phylogenetic relationships. Strain A7P-90m shared a low 16S rRNA sequence identity of around 85% with its closest relatives within the Bacteroides phylum. This low level of sequence similarity suggests that it may represent a novel family within this phylum. The 16S rRNA sequence identity between strain LZ-22 and its closest relatives Granulicoccus phenolivorans and Propioniferax innocua within the Propionibacteriaceae family were 91.9% and 93.2%, respectively. This low level of sequence similarity suggests that it may represent a novel genus within this family. Strains 9G and ISLP-3 were closely related to known species of the genera Halolactibacillus and Sanguibacter, respectively. However, the 16S rRNA sequence identities between strains 9G and ISLP-3 and their close relatives were too high to make reliable taxonomic inferences (i.e., 99.9% between 9G and H. miurensis, and 98.6% between ISLP-3 and S. suaresii). Because the recA gene delivers higher resolution for taxonomic inferences than the 16S rRNA gene, the primers for conserved recA gene were designed for PCR amplification and sequencing from Halolactibacillus and Sanguibacter type strains. Strain 9G shared a recA sequence identity of 99.6% with its closest relative H. miurensis, suggesting that it is a subspecies. The recA sequence identity shared between strain ISLP-3 and its six closest relatives ranged from 85.9~90.2%. This result is consistent with this strain representing a novel species within the genus Sanguibacter. Based on the molecular study presented here and the phenotypic properties presented elsewhere, we propose that strain LZ-22 is a representative of a novel genus and species, with proposed names Raineyella antarctica gen. nov., sp. nov. Strain ISLP-3 is a representative of a novel species, Sanguibacter gelidistatuaria sp. nov. Strain A7p-90m may represent a novel family within the order Bacteroidales. Chemotaxonomic characterizations of these strains are underway to gather more evidence for the proposed classifications.}, booktitle={Instruments, Methods, and Missions for Astrobiology XVII}, publisher={SPIE-Intl Soc Optical Eng}, author={Lyu, Zhe and Pikuta, Elena V. and Hagel, Jacob and LaBrake, Genevieve R. and Hoover, Richard B. and Whitman, William B.}, editor={Hoover, Richard B. and Levin, Gilbert V. and Rozanov, Alexei Yu. and Wickramasinghe, Nalin C.Editors}, year={2015}, month={Sep} }
 @article{liu_yang_lu_lu_2014, title={Response of a paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses}, volume={5}, url={http://aem.asm.org/content/early/2014/05/12/AEM.01259-14.abstract}, DOI={10.1128/AEM.01259-14}, abstractNote={ABSTRACT}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Liu, P. and Yang, Y. and Lu, Z. and Lu, Y.}, year={2014} }
 @article{lu_lu_2012, title={Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil}, volume={194}, DOI={10.1128/jb.00207-12}, abstractNote={ABSTRACT}, number={9}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Lu, Z. and Lu, Y.}, year={2012}, pages={2398–2399} }
 @article{methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from chinese rice field soil_2012, DOI={10.1371/journal.pone.0035279}, abstractNote={Background Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.). Methodology/Principal Findings By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254T was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAET was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4–2.8 µm long and by 0.2–0.3 µm in width. They grew at 37–60°C (optimally at 55°C) and salinity of 0–5 g NaCl l−1 (optimally at 0–1 g NaCl l−1). The pH range for growth was 6.4–7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5–7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254T utilized H2/CO2 but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254T and SANAET were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254T as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254T ( = CGMCC 1.5162T = JCM 17849T = DSM 24694T). Conclusions/Significance Strain HZ254T could potentially serve as an excellent laboratory model for studying Methanocellales due to its fast growth and consistent cultivability.}, year={2012} }
 @article{peng_lu_rui_lu_2008, title={Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil}, volume={74}, DOI={10.1128/aem.00070-08}, abstractNote={ABSTRACT}, number={9}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Peng, J. and Lu, Z. and Rui, J. and Lu, Y.}, year={2008}, pages={2894–2901} }