Program

The ever-growing demand of ecosystem goods and services, like marine food sources and recreation, inevitably requires actions to be taken to maintain good water quality and functional diversity of aquatic biota, which provide the foundation for ecosystem functioning and resilience. Water quality and functional diversity strongly depends on both, environmental conditions (e.g. local and global climate factors) and interacting species within and between communities (competition, predation etc.). These interactions, in turn, are limited by the genetic repertoire and phenotypic traits of each organism and population present within the particular habitat. Therefore, in order to sustainably manage our aquatic resources, there is a need for thorough understanding of the genetic basis of species interactions.
In the Baltic Sea eutrophication and over-fishing have been the foremost cause of ecosystem deterioration, characterized by increasing blooms of harmful filamentous cyanobacteria during summer-autumn months. Although many eco-physiological traits of major taxa of filamentous cyanobacteria (Aphanizomenon flos-aquae, Dolichospermum sp. and Nodularia spumigena) in the Baltic Sea, are well studied and understood, their interactions with co-occurring predators and, in particular, at the cellular and molecular levels remains elusive. Consequently, this precludes the conceptualization of cyanobacteria role in providing ecosystem goods and services. Therefore, I will summarise the current experimental and genome sequence data on filamentous cyanobacteria and their major predators (grazers and viruses) in the Baltic Sea, providing the mechanistic basis for better understand their interactions. These interactions can range from neutral to synergistic or antagonistic effects depending on the environmental conditions and co-occurring community. I will discuss these findings in the context of ecosystem services and will try to provide the necessary ecological context for better practice regarding management of ecosystem resources.

Viruses have considerable impact on the marine biogeochemical cycles through the process of virus-mediated microbial lysis. At the same time, continual host-phage interactions promote the emergence of defense systems against viruses to their hosts and viral counter-defense (co-evolution) that also generates their genetic diversity. Therefore, unveiling of diversity and dynamics of marine viruses, and their interaction with host is an important task for understanding of marine biological ecosystem. However, understanding of taxonomic diversity and ecology of viruses has been hampered by the lack of their universal gene.
Recent progress of next-generation sequencing technologies has allowed us to address a substantial amount of viral genomic data (virome) directly from marine viral assemblages. We recently obtained 1,352 environmental complete viral genomes representing 600 new viral genera. For instance, 54 of the genomes probably were derived from viruses infecting marine group II Euryarchaeota (MGII), for which no viruses have been isolated. Some genomes encoded Fe-S cluster synthesis genes (sufA and iscU), which may enhance viral adaptation. By recruitment of metagenomics and transcriptomic reads to these genomes, we have been able to evaluate dynamics of these viruses. This analysis showed that frequencies of novel viral genomes including MGII viruses were higher than those of previously known marine viruses. Their transcripts were observed in metatranscriptome of host fraction. Transciption patterns of the genomess depended on their predicted hosts rather than genomic contents of individual EVGs. Considering that host-selective phage infection influences and maintains bacterial abundance in a frequency-dependent way, where phage infection keeps in check the abundance of the fittest bacterial species (or strains), our results may also provide new insight into marine bacterial ecology (eg. MGII). Here, we will discuss what the viral metagenomics provide for future marine ecology and new marine genetic resources.

【Introduction】
Microcystis aeruginosa forms massive blooms in eutrophic freshwaters and are constantly exposed to lytic cyanophages. Cyanophages often carry host-derived genes to direct carbon flux from the Calvin cycle to pentose phosphate pathway, suggesting that cyanophages enhance production of energy (ATP) and reducing power (NADPH) to fuel dNTPs biosynthesis, thereby archive their efficient reproduction with maintaining host photosynthesis. Combination of the viral regulation and high proliferative capacity of cyanobacteria may be applicable to the production of valuable bioindustrial compounds. Here, we examined transcriptional dynamics and predicted primary sigma factor exploited by phage during Ma-LMM01 infection to elucidate viral regulation.
【Methods】
After inoculating the exponentially growing Microcystis cells with Ma-LMM01, infected cells were collected every 1 or 2 h from 0 to 24 h. Total RNA was extracted from the collected cells. After removeing rRNA, cDNA was synthesized from them. cDNA libraries were prepared using Nextera XT library preparation kit and sequenced with MiSeq. RNA-seq data were nomalized to gene length and library size (FPKM).
【Results and Discussion】
An average of one million reads were recovered from each cDNA library. The sequence reads were mapped to 4835 CDSs of NIES298 genome and 184 CDSs of Ma-LMM01 genome. Phage-derived reads slightly increased 0.13 % at 1 h, and then increased from 16% at 3 h to 33% at 6 h of total cellular reads. Almost all host genes (99%) did not show significant change in expression throughout infection. Phage gene dynamics showed three expression classes like lytic dsDNA phages including marine cyanophages; early (host-takeover), middle (replication) and late genes (virion morphogenesis). Although the recognition of middle and late promoter required host RNA polymerase modified by early gene products, bacterial RNA polymerase (sigma70) recognition-like sequences were also found in the upstream region of middle and late genes.

Carboxydotrophic microorganisms can grow on poisonous carbon monoxide (CO) because they possess CO dehydrogenases (CODH), which catalyze the interconversion of CO₂ and CO. CODHs are involved in several important metabolic activities such as energy conservation and carbon fixation. Hydrogenogenic carboxydotrophs (CO trophs) possess a CODH gene clustered with hydrogenase genes, and can acquire energy via CO oxidation and H₂ generation. Therefore, hydrogenogenic CO trophs can be considered candidate biocatalysts for improving the efficiency of H₂ production from syngas. Further, CO is the most important precursor for C1-chemistry. CODHs can be new sustainable catalysts for generating CO from CO₂
. However, knowledge on diverse CO trophs is limited, and this creates a bottleneck for the development of efficient biocatalysts and catalysts.
We have successfully isolated various thermophilic hydrogenogenic CO trophs from oceanic and terrestrial hydrothermal environments. Of these, one particular bacterium of novel genera, isolated from a core sample of a submerged caldera, harbors six CODH genes. This bacterium appears to be an “ancient-type” CO troph that had been dormant in the core as spores, and is a powerful CO utilizer. Now we are working on comprehensive understanding of the CO trophs, particularly “ancient-types”, towards construction of a next-generation platform for CO₂ reduction and carbon cycle through below studies.
1.Isolation of various CO trophs from water and core samples of oceanic and terrestrial hydrothermal environments and investigate their genetic diversity by metagenomic analysis.
2.Analysis of CO metabolism of the unique carboxydotrophic isolates by genomic, metabolomic, and transcriptomic analysis.
3.Characterization of recombinants carrying efficient CODH, and construct a large expression system for the CODH.
Here we will discuss what understanding CO trophs and their CO metabolism will provide for our future platform for CO₂ reduction and carbon cycle.

A thermophile Calderihabitans maritimus KKC1 (KKC1) isolated from a submerged marine caldera can grow on carbon monoxide (CO) (carboxydotrophic) and produce hydrogen as a byproduct (hydrogenogenic). Here, we describe the de novo sequencing and feature analysis of the KKC1 genome. Genome-based phylogenetic analysis confirmed that KKC1 was most closely related to the genus Moorella which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella species, KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin. KKC1 lacked the HydABC and NfnAB electron bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction during acetogenic growth. Furthermore, KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Of six CooS genes of KKC1, three formed known gene clusters in other microorganisms: cooS−acetyl-CoA synthase, cooS−energy-converting hydrogenase, and cooF−cooS−FAD-NAD oxidoreductase, while the other three had novel genomic contexts. According to phylogenetic analysis of CooS genes, two cooS genes with novel genomic contexts were classified into “Clade B” and “Clade C”, respectively, and the other four cooS genes were classified into “Clade F”. Sequence composition analysis indicated that these cooS genes likely evolved from a common ancestor. Collectively, these data suggest that KKC1 may be highly dependent on CO as a low potential electron donor to directly reduce ferredoxin and more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which solve the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen by using bifurcating enzymes.

Mangrove forest ecosystems that are the interface ecosystems between land and sea in the tropical region are ecologically important habitats for diverse species of birds, fishes, crustaceans and other animals. The ecosystems also represent one of the most dynamic and diverse microbial habitats, indicating the ecosystems have potential resources for novel microorganisms and secondary metabolites. Malaysian mangrove is the third largest mangrove in Asia-Pacific area. However, the microbial studies in Malaysian mangrove are still scarce. In this study, we focus on the Matang Mangrove Forest Reserve (MMFR) in Malaysia and analyzed high-throughput metagenomic datasets from two distinct sites at MMFR, the Virgin Jungle Forest (VJF) and the harvested Productive Zone (PV).
Physicochemical properties of soil samples from VJF and PZ are quite similar except total organic carbon contents. The total organic carbon content in PZ was 18.7 times higher than that of VJF. Taxonomic classification of sequencing reads using metagenomics RAST revealed that the Productive Zone metagenome exhibited Bacteroidetes and Firmicutes as the prominent phylum. Many bacterial species including these phylums are known as polysaccharide-degrading bacteria. Functional profiles of the metagenomics sequences revealed that genes encoding enzymes for the degradation of plant cell wall polysaccharides, such as hemicellulose, were abundantly found in the PZ sample. These results were consistent with the soil physicochemical property of PZ in which the soil contains high organic carbon.
At the same time, we isolated over 250 bacterial strains from soil samples of VJF and PZ. A novel xylan-degrading bacterium belonging to the genus Mangrovimonas was isolated and named as Mangrovimonas xylaniphaga sp. This strain possesses many xylan–degrading enzymes. Besides that, several novel bacterial species were also identified. These indicate that Malaysian mangrove is a potential resource for beneficial genes and novel bacterial species.