Michael Visser

Bio: Michael Visser is an academic researcher from Wageningen University and Research Centre. The author has contributed to research in topics: Desulfotomaculum & Genome. The author has an hindex of 8, co-authored 15 publications receiving 245 citations. Previous affiliations of Michael Visser include VU University Medical Center.

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum strain SIT.

Abstract: Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3,567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism.

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways.

Abstract: Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17T, isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

Abstract: Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

Bacillus subtilis. (Book Reviews: The Molecular Biology of the Bacilli; Molecular Cloning and Gene Regulation in Bacilli)

Abstract: К пробиотикам относят «живые микроорганизмы, которые при введении в адекватных количествах оказывают положительное влияние на здоровье хозяина» [1]. В то время как применению некоторых из них (Lactobacillus, Bifidobacterium) было уделено много внимания, другие были изучены позже, и их важное лечебное действие становится ясным только сейчас. Одним из пробиотиков является грамположительная палочка Bacillus subtilis (B.subtilis). Большинство бактерий рода Bacillus (включая B.subtilis) не опасны для человека и широко распространены в окружающей среде. Их обнаруживают в почве, воде, воздухе и пищевых продуктах (пшеница, другие зерновые культуры, хлебобулочные изделия, соевые продукты, цельное мясо, сырое и пастеризованное молоко). Как следствие, они постоянно попадают в желудочно-кишечный тракт и дыхательные пути, засевая эти отделы. Количество бацилл в кишечнике может достигать 10 КОЕ/г, что сравнимо с аналогичным показателем у Lactobacillus. В связи с этим ряд исследователей рассматривают бактерии рода Bacillus как один из доминирующих компонентов нормальной микрофлоры кишечника [2]. В то же время лечебное введение B.subtilis позволяет использовать данный микроорганизм в качестве пробиотика по четырем основным направлениям: 1) для защиты от кишечных патогенов; 2) от дыхательных патогенов; 3) для устранения дисбактериоза при антибиотикотерапии; 4) для усиления переваривания и продвижения пищи. Упрощенная схема пробиотической активности B.subtilis при патологии желудочнокишечного тракта представлена на рис. 1. Таким образом, в научных работах последних десятилетий были сделаны значительные продвижения в выяснении спектра пробиотической активности B.subtilis, что делает данную бактерию одним из наиболее привлекательных пробиотиков для медицинского применения. В настоящем обзоре мы представляем данные соответствующих экспериментальных и клинических исследований, позволяющих составить впечатление о терапевтическом потенциале B.subtilis. УДК 615.331:579.852.1

Reverse Methanogenesis and Respiration in Methanotrophic Archaea.

Abstract: Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Abstract: Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.