Gerard Muyzer

University of Amsterdam | UVA · Institute for Biodiversity and Ecosystem Dynamics

Caulerpa is a genus of green macroalgae that lives in tropical and subtropical coastal waters. It is an intriguing organism because, despite having plant-like structures, it is one giant cell – which, next to multiple nuclei, chloroplasts, and mitochondria, also contains endo- and epiphytic bacteria. The role of these bacteria is unknown, but they...

Here, we present the draft genome sequence of Alteromonas gracilis strain J4, isolated from the green macroalga Caulerpa prolifera. The draft genome is 4,492,914 bp in size and contains 4,719 coding DNA sequences, 67 tRNAs, and 16 rRNA-coding genes. Strain J4 may exhibit host growth-promoting properties.

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina , a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. D...

Introduction Many coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether...

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial co...

Haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio are highly abundant in microbial communities found in soda lakes and dominant in full-scale bioreactors removing sulfide from industrial waste gases. Despite certain soda lakes being remote and unaffected by anthropogenic activities, haloalkalip...

Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which...

Human-driven changes affect nutrient inputs, oxygen solubility and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-tran...

The holopelagic brown macroalgae Sargassum natans and Sargassum fluitans form essential habitats for attached and mobile fauna which contributes to a unique biodiversity in the Atlantic Ocean. However, holopelagic Sargassum natans (genotype I & VIII) and Sargassum fluitans (genotype III) have begun forming large accumulations with subsequent strand...

Background Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in...

Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review d...

The ability of organisms to combine autotrophy and heterotrophy gives rise to one of the most successful nutritional strategies on Earth: mixotrophy. Sponges are integral members of shallow-water ecosystems and many host photosynthetic symbionts, but studies on mixotrophic sponges have focused primarily on species residing in high-light environment...

Marine ecosystems are among the largest aquatic ecosystems on Earth. They harbor a wealth of biodiversity, provide essential ecosystem services, and are a rich source of bioproducts. Within these marine ecosystems, microorganisms play a crucial role in recycling chemical elements such as carbon, nitrogen, and sulfur. It has become increasingly reco...

In biodesulfurization (BD) at haloalkaline and dO 2 -limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten rea...

Marine sponges play a major ecological role in recycling resources on coral reef ecosystems. The cycling of resources may largely depend on the stability of the host–microbiome interactions and their susceptibility to altered environmental conditions. Given the current coral-to-algal phase shift on coral reefs, we investigated whether the sponge-as...

While processes involved in the protohistoric briquetage at Puntone (Tuscany, Italy) have been reconstructed in detail, the age of this industry remained uncertain since materials suited for traditional dating (14 C dating on charcoal and typological dating of ceramics) were very scarce. We attempted to assess its age by radiocarbon dating organic...

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked....

Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community compos...

Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge‐associated community structure with DOM utilization is essential to understand host–microbe interactions in the uptake, processing, and exchange of resources. We coupled,...

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of tw...

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

Background Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities....

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Thi.o.halo.mo'nas Gr. neut. n. thion sulfur; Gr. masc. n. hals, halos salt of the sea; Gr. fem. n. monas unit, monad; N.L. fem. n. Thiohalomonas halophilic sulfur‐utilizing monad. Proteobacteria / Gammaproteobacteria / “Thiohalomonadales” / “Thiohalomonadaceae” / Thiohalomonas The genus Thiohalomonas was originally classified as a member of an unaf...

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water (PW) of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of PCR-a...

Thi.o.ha.lo'phi.lus. Gr. neut. n. thion sulfur; Gr. masc. n. hals, halos salt of the sea; Gr. masc. adj. philos loving; N.L. masc. n. Thiohalophilus sulfur and salt loving. Proteobacteria / Gammaproteobacteria / “Thiohalomonadales” / “Thiohalophilaceae” / Thiohalophilus The genus Thiohalophilus was originally classified as an unaffiliated member of...

Thi.o.ha.lo.spi'ra. Gr. neut. n. thion sulfur; Gr. masc. n. hals, halos salt of the sea; L. fem. n. spira spiral; N.L. fem. n. Thiohalospira salt‐loving sulfur spiral. Proteobacteria / Gammaproteobacteria / “Thiohalospirales” / “Thiohalospiraceae” / Thiohalospira The genus Thiohalospira was originally classified as a member of the family Ectothiorh...

Modern stromatolites are key to the record of past microbial activity preserved in fossil carbonate deposits. Mono-phototrophic cultures dominated by the cyanobacterium Geitlerinema sp. were obtained from a laboratory-maintained, low magnesium-calcite stromatolite originating from Lagoa Vermelha, Brazil. This lagoonal system has been described as a...

Thi.o.halo.bac'ter. Gr. neut. n. thion sulfur; Gr. masc. n. hals, halos salt of the sea; N.L. masc. n. bacter a rod; N.L. masc. n. Thiohalobacter halophilic sulfur rod. Proteobacteria / Gammaproteobacteria / Thiohalobacterales / Thiohalobacteraceae / Thiohalobacter The genus Thiohalobacter was originally classified as an unaffiliated member of an d...

Thi.o.ha.lo.rhab'dus. Gr. neut. n. thion sulfur; Gr. masc. n. hals, halos salt of the sea; Gr. fem. n. rhabdos rod, stick; N.L. fem. n. Thiohalorhabdus halophilic sulfur rod. Proteobacteria / Gammaproteobacteria / Thiohalorhabdales / Thiohalorhabdaceae / Thiohalorhabdus The genus Thiohalorhabdus was originally classified as a deep unaffiliated line...

Thi.o.al.ka.li.bac'ter Gr. neut. n. thion sulfur; M.L. n. alkali (from Arabic al‐qalyi, the ashes of saltwort) soda ash; N.L. masc. n. bacter a rod; N.L. masc. n. Thioalkalibacter rod‐shaped bacterium that loves alkaline conditions and utilizes sulfur compounds. Proteobacteria / Gammaproteobacteria / Halothiobacillales / Salinibacteraceae / Thioalk...

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from t...

Exposing a microbial community to alternating absence and presence of carbon substrate in aerobic conditions is an effective strategy for enrichment of storage polymers (polyhydroxybutyrate, PHB) producing microorganisms. In this work we investigate to which extent intermediate storage polymer production is a temperature independent microbial compe...

Background: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we in...

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern Calif...

Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in grou...

The genomes of Thiohalobacter thiocyanaticus and Guyparkeria (formerly known as Halothiobacillus) sp. SCN-R1, two gammaproteobacterial halophilic sulfur-oxidizing bacteria (SOB) capable of thiocyanate oxidation via the “cyanate pathway”, have been analyzed with a particular focus on their thiocyanate-oxidizing potential and sulfur oxidation pathway...

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M...

The existence of sulfate-reducing bacteria (SRB) is a major concern in oil industry due to the detrimental effects of SRB in oil technology. SRB are co-habited with diverse microbial populations in oil fields. The presence of other bacterial groups in oil fields may alter SRB activity in different ways. Therefore, understanding this coexistence may...

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for...

Maximum likelihood tree of SoxY sequences, based on 500 bootstrap replicates. Sequences of desulfoferredoxin-family proteins were used as the outgroup and pruned from the tree. The scale bar represents % difference.

Maximum likelihood tree of SoxZ sequences, based on 500 bootstrap replicates. Sequences of quinoprotein dehydrogenase-associated SoxYZ-like proteins were used as outgroup and later pruned from the tree. The scale bar represents % differences.

Maximum likelihood tree of SoeA sequences, based on 500 bootstrap replicates. Sequences of sulfite:cytochrome c oxidoreductase subunit A (SorA) were used as outgroup and pruned from the tree. The scale bar represents % differences. Bootstrap values below 50% are not shown. Parenthesized numbers indicate the number of sequences included in a collaps...

Overview of Thioalkalivibrio strains included in this study, including geographical location from which the strain was isolated, genome size, number of protein-coding genes, genome accession number and the results of the CheckM analysis.

Groups of orthologous proteins as predicted by OrthoMCL. Rows represent the different ortholog groups. Accession numbers of protein sequences included in an ortholog group are separated by tabs on the same line.

The input of nutrients from anthropogenic sources is the leading cause of coastal eutrophication and is usually coupled with algal/seaweed blooms. Effects may be magnified in semi-enclosed systems, such as highly productive coastal lagoon ecosystems. Eutrophication and seaweed blooms can lead to ecosystem disruption. Previous studies have considere...

Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism...

Background: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencin...

Seagrasses play an important role as ecosystem engineers; they provide shelter to many animals and improve water quality by filtering out nutrients and by controlling pathogens. Moreover, their rhizosphere promotes a myriad of microbial interactions and processes, which are dominated by microorganisms involved in the sulfur cycle. This study provid...

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) drive major transformations in the sulfur cycle, and play vital roles in oxic-anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we use...

Thiocyanate (N=C-S-) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolatecontaining plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and...

Although bacteria play key roles in aquatic food webs and biogeochemical cycles, information on the seasonal succession of bacterial communities in lakes is still far from complete. Here, we report results of an integrative study on the successional trajectories of bacterial communities in a seasonally stratified lake with an anoxic hypolimnion. Th...

Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs...