Article
Environmental Sciences
Reka Hajdu-Rahkama, Bestamin Ozkaya, Aino-Maija Lakaniemi, Jaakko A. Puhakka
Summary: The aim of this study was to investigate the potential for elemental sulphur recovery from sulphurous solutions under aerobic and anoxic conditions by haloalkalophilic Thioalkalivibrio denitrificans. The results showed that high-rate aerobic biotransformation kinetics of thiosulphate were demonstrated, whereas the rates were slower and no S-0 accumulated under anoxic conditions. Thus, future developments of biotechnical applications for the recovery of S-0 from haloalkaline streams from the process industry should focus on aerobic treatment.
ENVIRONMENTAL TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Sumit Peh, Tingzhen Mu, Wei Zhong, Maohua Yang, Zheng Chen, Gama Yang, Xuhao Zhao, Moustafa Mohamed Sharshar, Nadia A. Samak, Jianmin Xing
Summary: This study investigates the use of a fluidic oscillation aeration system to enhance the biodesulfurization process in an airlift bioreactor. The results show that the microbubble strategy in the airlift bioreactor achieved a higher yield and selectivity of biological sulfur compared to a bubble column bioreactor. The study also reveals the biodesulfurization conditions for thiosulfate using Thioalkalivibrio versutus D306.
Article
Multidisciplinary Sciences
Yee Wen Low, Sitaram Rajaraman, Crystal M. Tomlin, Joffre Ali Ahmad, Wisnu H. Ardi, Kate Armstrong, Parusuraman Athen, Ahmad Berhaman, Ruth E. Bone, Martin Cheek, Nicholas R. W. Cho, Le Min Choo, Ian D. Cowie, Darren Crayn, Steven J. Fleck, Andrew J. Ford, Paul Forster, Deden Girmansyah, David J. Goyder, Bruce Gray, Charlie D. Heatubun, Ali Ibrahim, Bazilah Ibrahim, Himesh D. Jayasinghe, Muhammad Ariffin Kalat, Hashendra S. Kathriarachchi, Endang Kintamani, Sin Lan Koh, Joseph T. K. Lai, Serena M. L. Lee, Paul K. F. Leong, Wei Hao Lim, Shawn K. Y. Lum, Ridha Mahyuni, William J. F. McDonald, Faizah Metali, Wendy A. Mustaqim, Akiyo Naiki, Kang Min Ngo, Matti Niissalo, Subhani Ranasinghe, Rimi Repin, Himmah Rustiami, Victor Simbiak, Rahayu S. Sukri, Siti Sunarti, Liam A. Trethowan, Anna Trias-Blasi, Thais N. C. Vasconcelos, Jimmy F. Wanma, Pudji Widodo, Douglas Siril A. Wijesundara, Stuart Worboys, Jing Wei Yap, Kien Thai Yong, Gillian S. W. Khew, Jarkko Salojarvi, Todd P. Michael, David J. Middleton, David F. R. P. Burslem, Charlotte Lindqvist, Eve J. Lucas, Victor A. Albert
Summary: This study demonstrates the contribution of neutral forces to the species radiation of the tree genus Syzygium. By combining reference genome assembly and population genetics analyses, the authors reveal the importance of neutral processes in driving the diversification of Syzygium.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Tingzhen Mu, Maohua Yang, Jianmin Xing
Summary: This study developed a bio-desulfurizing system based on a sulfur-oxidizing bacterium under haloalkaliphilic conditions, demonstrating optimal performance under specific sulfide load and ORP values, as well as revealing spatial and temporal heterogeneity in the bioreactor. The study also emphasized the key role of operating conditions in shaping sulfur particle morphology and highlighted the efficiency of gravity settling for particle harvesting. The findings provide valuable insights for the design and optimization of industrial bio-desulfurizing equipment in the future.
BIOCHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Tamara V. Tikhonova, Anastasiya V. Lilina, Evgenii M. Osipov, Nikolay S. Shipkov, Nataliya I. Dergousova, Olga G. Kulikova, Vladimir O. Popov
Summary: The flavocytochrome c sulfide dehydrogenase (FCC) is a key enzyme in sulfur-oxidizing bacteria for oxidizing sulfide. Thioalkalivibrio paradoxus ARh1 genome contains multiple homologous FCC genes that play different roles in the bacterium when growing on sulfide as the main energy source.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Microbiology
Katherine C. Crosby, Mariah Rojas, Parul Sharma, Marcela A. Johnson, Reza Mazloom, Brian H. Kvitko, Theo H. M. Smits, Stephanus N. Venter, Teresa A. Coutinho, Lenwood S. Heath, Marike Palmer, Boris A. Vinatzer
Summary: This study establishes a core genome tree for the genus Pantoea, covering the known diversity of this genus. By integrating with metadata, literature, and nomenclature, the research successfully describes each species and significant genetic lineage.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jean-Pierre Peros, Amandine Launay, Andre Peyriere, Gilles Berger, Catherine Roux, Thierry Lacombe, Jean-Michel Boursiquot
Summary: By analyzing the genetic diversity and morphological traits of 90 accessions of Vitis species and hybrids, we identified three clades in North America, one in East Asia, and one in Europe corresponding to V. vinifera. We also found evidence of hybridization and significant correlations between traits and phylogeny. The American clade, including important species like V. riparia and V. rupestris, showed significant divergence from other clades.
Article
Biochemistry & Molecular Biology
Takushi Kishida, Mamoru Toda, Yasuhiro Go, Shoji Tatsumoto, Takahide Sasai, Tsutomu Hikida
Summary: Speciation in the open ocean, specifically among marine amniotes like sea snakes, is a complex process influenced by factors like genetic isolation and gene flow. Despite having similar aquatic origins, Laticauda species have rarely speciated due to broad distribution of major species and genetic mixability, which inhibit genetic isolation. The study highlights the importance of considering demographic history and genetic diversity in understanding speciation patterns in the open ocean.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia Leon, Shawn M. Kaeppler, C. Robin Buell
Summary: High-quality genome assemblies of maize stiff-stalk inbreds were created, revealing extensive collinearity among these inbreds and unique components in the maize pangenome. While representing only a proportion of variation in the original stiff-stalk pool, these inbreds showed significant genetic and genomic variation, supporting the potential for continued breeding success in this pool.
Article
Plant Sciences
Fabio Palumbo, Samela Draga, Francesco Scariolo, Giovanni Gabelli, Gio Batta Sacilotto, Marco Gazzola, Gianni Barcaccia
Summary: In this study, the genetic knowledge and taxonomic gaps in the Mandevilla genus were addressed by analyzing 55 accessions. The genomes of a reference sample were analyzed, resulting in the determination of the triploid genome size, assembly of the plastidial genome, and a draft of the nuclear genome. The study also identified proteins involved in the biosynthesis of plant compounds. Furthermore, SSR markers were developed and used to validate the Mandevilla collection. The study provided insights into the origin, divergence, and relationships among the studied accessions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Aleksandar Stanojkovic, Svatopluk Skoupy, Pavel Skaloud, Petr Dvorak
Summary: The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, insufficient population-level sampling has hindered the study of intra-species genetic diversity and speciation in cyanobacteria. In this study, using phylogenomics and a population genomic approach, the authors investigated the extent of local genomic diversity and the mechanisms underlying sympatric speciation in Laspinema thermale. They found two cryptic lineages of Laspinema with high genetic diversity. Recombination occurred more frequently within the lineages, suggesting a barrier to gene flow that maintains divergence. Genomic regions associated with possible adaptations to different environmental conditions were found, indicating the influence of both genomic and ecological processes on Laspinema species diversification.
FRONTIERS IN MICROBIOLOGY
(2022)
Editorial Material
Genetics & Heredity
Segun Fatumo, Aminu Yakubu, Olubukunola Oyedele, Jumi Popoola, Delali Attiogbe Attipoe, Golibe Eze-Echesi, Fatima Z. Modibbo, Nabila Ado-Wanka, Omolola Salako, Oyekanmi Nashiru, Babatunde L. Salako, Colm O'Dushlaine, Abasi Ene-Obong
Summary: The Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) consortium was established to create a comprehensive catalog of human genetic variation in Nigeria and analyze the burden and etiological characteristics of non-communicable diseases in 100,000 adults.
Article
Multidisciplinary Sciences
Srishti Chaudhary, Ramandeep Singh, Sukrampal Yadav, Sunil A. Patil
Summary: Electrotrophic microorganisms in extreme environments, such as the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment studied in this research, demonstrate efficient nitrate reduction through direct-contact cathodic electron uptake, indicating potential roles in nitrogen cycling in such environments. The enriched biofilm exhibited high current density and nitrate reduction efficiency, with the presence of unreported bacterial species identified through amplicon sequencing.
Article
Environmental Sciences
Lei Gao, Bao-Zhu Fang, Chun-Yan Lu, Kun-Hui Hong, Xin-Yu Huang, Ting-Ting She, Min Xiao, Wen-Jun Li
Summary: During an investigation of microbial diversity in sediments, seven strains of Demequina were found. These strains have the potential to degrade complex carbon sources and oxidize sulfides, and provide insights into their metabolic model and ecological roles.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Microbiology
Ruizhe Guo, Kaiyang Zheng, Lin Luo, Yundan Liu, Hongbing Shao, Cui Guo, Hui He, Hualong Wang, Yeong Yik Sung, Wen Jye Mok, Li Lian Wong, Yu-Zhong Zhang, Yantao Liang, Andrew McMinn, Min Wang
Summary: A novel single-stranded DNA phage, vB_VpaM_PG19, infecting V. parahaemolyticus, was isolated and it represents a potential antimicrobial agent for pathogenic V. parahaemolyticus. It might belong to a new viral genus called Vimicrovirus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Meggie Hudspith, Laura Rix, Michelle Achlatis, Jeremy Bougoure, Paul Guagliardo, Peta L. Clode, Nicole S. Webster, Gerard Muyzer, Mathieu Pernice, Jasper M. de Goeij
Summary: Sponges are recognized as key ecosystem engineers in aquatic habitats, with the ability to process organic matter efficiently. Through experiments, it is found that microbial communities in high and low microbial abundance sponges interact with hosts in nutrient exchange and symbiotic relationships.
Article
Microbiology
Anne-Catherine Ahn, Evelien Jongepier, J. Merijn Schuurmans, W. Irene C. Rijpstra, Jaap S. Sinninghe Damste, Erwin A. Galinski, Pawel Roman, Dimitry Sorokin, Gerard Muyzer
Summary: The Thioalkalivibrio bacteria genus adapts to various extreme parameters, including low temperature, in soda lakes. Two strains from soda lakes with different temperature regimes showed similar molecular and physiological adaptation responses to low temperature, utilizing resistance mechanisms against other stressors commonly found in soda lakes. The strain AL2(T) grew faster at 10 degrees C due to higher glycine betaine content, while both strains exhibited changes in membrane lipid composition and upregulated genes involved in cold adaptation.
Article
Microbiology
Sara Campana, Kathrin Busch, Ute Hentschel, Gerard Muyzer, Jasper M. de Goeij
Summary: This study used DNA stable isotope probing and 16S rRNA amplicon sequencing to identify metabolically active bacterial taxa involved in dissolved organic matter (DOM) uptake in a sponge holobiont. The results revealed that specific bacterial taxa belonging to PAUC34f, Poribacteria, and Chloroflexi phyla are active consumers of DOM through heterotrophic carbon metabolism, while Nitrospirae may have mixotrophic capabilities. This research provides new insights into the interaction between diverse sponge-associated bacteria and DOM consumption in marine ecosystems.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Suyash Gupta, Caroline M. Plugge, Johannes B. M. Klok, Gerard Muyzer
Summary: In this study, the bacterial composition of the biodesulfurization process was analyzed using 16S rRNA gene sequencing. Thioalkalivibrio sulfidiphilus was found to be the dominant species, consistent with previous studies. The composition of the feed gas and its components had a significant impact on the microbial community composition.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jan P. Meier-Kolthoff, Joaquim Sarda Carbasse, Rosa L. Peinado-Olarte, Markus Goeker
Summary: Microbial systematics is influenced by genome-based methods and faces challenges from the increasing number of taxon names and associated sequences. Accurate and reliable high-throughput platforms like LPSN and TYGS are essential for handling the data efficiently. The updates include new features and expanded database content to provide easy access to the data.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Hao Li, Jan P. Meier-Kolthoff, Canxin Hu, Zhongjie Wang, Jun Zhu, Wei Zheng, Yun Tian, Feng Guo
Summary: This study investigates the evolutionary history, host specificity, and biogeographic distribution of Prevotella copri and its related taxa. It found that P. copri in the human gut consists of multiple groups with high genomic divergence and non-strict biogeographic patterns. It also reveals long-term co-evolution between P. copri and higher primates, but also sporadic signals of co-speciation and extensive host jumping. Furthermore, the study highlights extensive horizontal transfer of genes among P. copri groups and species in the same primate host.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Ecology
Meggie Hudspith, Jasper M. de Goeij, Mischa Streekstra, Niklas A. Kornder, Jeremy Bougoure, Paul Guagliardo, Sara Campana, Nicole N. van der Wel, Gerard Muyzer, Laura Rix
Summary: The ability of organisms to combine autotrophy and heterotrophy gives rise to the successful nutritional strategy of mixotrophy. This study focuses on the contribution of photoautotrophy to the respiratory demand and carbon diet of the sponge Chondrilla caribensis in low-light environments. The findings suggest that photoautotrophy can provide an important supplemental source of carbon for sponges residing in low-light habitats.
Review
Biotechnology & Applied Microbiology
Xi Bai, Inez J. T. Dinkla, Gerard Muyzer
Summary: Biofiltration is a crucial water treatment technology for producing safe drinking water. It is gaining worldwide interest due to its advantages of no chemical addition, low energy input, and high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. This review highlights the microbial ecology of three commonly used biofiltration processes in drinking water treatment plants and summarizes their characteristics, removal performance, and newly revealed mechanisms. It also discusses the role of microbial communities in removing nutrients, organic compounds, and pathogens, and suggests future perspectives for a comprehensive understanding of the microbial ecology of biofiltration.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Alberto J. Martin-Rodriguez, Jan P. Meier-Kolthoff
Summary: The family Shewanellaceae comprises three genera, Shewanella, Parashewanella and Psychrobium. The discovery of new species within this family has been steadily increasing in recent years, indicating that the true diversity of this family has only just begun to be revealed. Through sequencing of Shewanella type strains lacking publicly available whole-genome sequences, we have provided a comprehensive taxonomy of Shewanella and Parashewanella, identifying 48 novel species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Sara Campana, Ana Riesgo, Evelien Jongepier, Janina Fuss, Gerard Muyzer, Jasper M. de Goeij
Summary: This study investigates the differential gene expression of two sponge holobionts after feeding on coral- and macroalgal-DOM sources. The results show that there are slight but significant differences in gene expression between the two treatments in both high and low microbial abundance sponges. Processes related to immune response, signaling pathways, and metabolic pathways were regulated in the hosts, while carbohydrate metabolism was upregulated in the associated microbiota. This study provides insights into the metabolic activity of sponge holobionts in response to different DOM sources.
Article
Microbiology
Maria del Carmen Montero-Calasanz, Adnan Yaramis, Manfred Rohde, Peter Schumann, Hans-Peter Klenk, Jan P. Meier-Kolthoff
Summary: Integrating genomic information into microbial systematics allows for reliable prokaryotic classification. In silico chemotaxonomic analysis is being introduced to replace traditional laboratory methods for characterizing taxa, increasing speed and accuracy of taxonomic reports. Genomics has already played a role in taxonomic rearrangement, highlighting the need for revisiting taxonomy in light of new genomic data.
FRONTIERS IN MICROBIOLOGY
(2022)
Correction
Microbiology
Maria del Carmen Montero-Calasanz, Adnan Yaramis, Manfred Rohde, Peter Schumann, Hans-Peter Klenk, Jan P. Meier-Kolthoff
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Xi Bai, Inez J. T. Dinkla, Gerard Muyzer
Summary: This study found that both DNA and RNA data should be considered when studying the microbial communities in slow sand filters (SSF). The microbial communities in the Schmutzdecke layer were influenced by the influent water and shared a core microbiome among different filters. Indicator organisms associated with the age of Schmutzdecke were also identified.
Article
Microbiology
Muhe Diao, Cherel Balkema, Maria Suarez-Munoz, Jef Huisman, Gerard Muyzer
Summary: Changes in stratification and mixing events have a significant impact on the nitrogen cycle of seasonally stratified lakes. This study investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months and found that their abundance and activity varied with the seasonal stratification pattern. The results suggest that global warming-induced changes in stratification and vertical mixing are likely to alter the nitrogen cycle of seasonally stratified lakes.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Biotechnology & Applied Microbiology
Suyash Gupta, Rieks de Rink, Johannes B. M. Klok, Gerard Muyzer, Caroline M. Plugge
Summary: This study identified the active microbial community members in the BD system by comparing DNA-based and RNA-based sequencing results, and found that the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor played a significant role in shaping the microbial communities.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
