Sex: Male

Education:
Doctor of Philosophy in Biological Sciences, Tokyo Metropolitan University, 2019
Bachelor of Science in Biology, University of the Philippines Visayas, 1999

Field of Specialization:
Environmental microbiology
Gel Electrophoresis
Microbial Biotechnology
Microbial Culture
Microbial Isolation
General Microbiology
DNA
Bacteriology
DNA Extraction

Researches:

Article title: Draft Genome Sequence of the Thermophilic Unicellular Cyanobacterium Synechococcus sp. Strain C9
Authors: Megumi Kono, Joval N. Martinez, Takeshi Sato, Shin Harutaa
Publication title: Microbiology Resource Announcements 11(8), July 2022

Abstract:
This study presents the genome sequence of Synechococcus sp. strain C9 (= CCMEE 5213 = ATCC 700244), a thermophilic unicellular cyanobacterium that was originally isolated from a thermal pool at Octopus Spring, Yellowstone National Park, USA. The genome consists of a 2,958,309-bp chromosome with a GC content of 52.9% and 2,854 protein-coding sequences
Full text link https://tinyurl.com/4hufkpam

Article title: Metagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, Japan
Authors: Joval Navas Martinez, Arisa Nishihara, Shin Haruta
Publication title: Microbiology Resource Announcements 10(38), September 2021

Abstract:
Draft genome sequences of putatively novel bacteria were assembled from the metagenome of epilithic biofilm samples collected from the Tama River (Tokyo, Japan). The metagenome contains 44,630,724 sequences, 44,792 contigs, and 48% G+C content. Binning resulted in 31 metagenome-assembled genomes (MAGs) with >50% completeness.
Full text link https://tinyurl.com/navnj48m

Article title: In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat
Authors: Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Küh, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada and Vera Thiel
Publication title: Microorganisms 9(3):652, March 2021

Abstract:
Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.
Full text link https://tinyurl.com/2p89uu9d

Article title: Draft Genome Sequence of a Filamentous Anoxygenic Phototrophic Bacterium, "Candidatus Roseilinea sp. Strain NK_OTU-006," Recovered from Metagenomic Data of a Hot Spring Microbial Mat
Authors: Joval N. Martinez, Shigeru Kawai, Mohit Kumar Saini,aMarcus Tank, Satoshi Hanada, Vera Thiel
Publication title: Microbiology Resource Announcements 9(50):3, December 2020

Abstract:
We report here the metagenome-assembled draft genome of an uncul-tured filamentous anoxygenic phototroph of the phylum Chloroflexota (formerly Chloroflexi), "Candidatus Roseilinea sp. strain NK_OTU-006," recovered from hot spring-associated microbial mats. The 3.6-Mb genome is estimated to be 94% complete and comprises 117 contigs encoding 3,203 predicted genes, including a full-length rRNA operon.
Full text available upon request to the author/s.

Article title: Vertical Distribution and Diversity of Phototrophic Bacteria within a Hot Spring Microbial Mat (Nakabusa Hot Springs, Japan)
Authors: Joval Navas Martinez, Arisa Nishihara, Mads Lichtenberg, Erik Trampe, Shigeru Kawai, et al.
Publication title: Microbes and Environments 34(4), November 2019

Abstract:
Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated them with microsensor measurements of O2 and spectral scalar irradiance. A stable core community and high diversity of phototrophic organisms dominated by the filamentous anoxygenic phototrophs, Roseiflexus castenholzii and Chloroflexus aggregans were identified together with the spectral signatures of bacteriochlorophylls (BChls) a and c absorption in all mat layers. In the upper mat layers, a high abundance of cyanobacteria (Thermosynechococcus sp.) correlated with strong spectral signatures of chlorophyll a and phycobiliprotein absorption near the surface in a zone of high O2 concentrations during the day. Deeper mat layers were dominated by uncultured chemotrophic Chlorobi such as the novel putatively sulfate-reducing “Ca. Thermonerobacter sp.”, which showed increasing abundance with depth correlating with low O2 in these layers enabling anaerobic metabolism. Oxygen tolerance and requirements for the novel phototroph “Ca. Chloroanaerofilum sp.” and the uncultured chemotrophic Armatimonadetes member type OS-L detected in Nakabusa hot springs, Japan appeared to differ from previously suggested lifestyles for close relatives identified in hot springs in Yellowstone National Park, USA. The present study identified various microenvironmental gradients and niche differentiation enabling the co-existence of diverse chlorophototrophs in metabolically diverse communities in hot springs.
Full text link https://tinyurl.com/35dspdz9

Article title: “Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities
Authors: Vera Thiel, Amaya M. Garcia Costas, Nathaniel W. Fortney, Joval N. Martinez, Marcus Tank, Eric E. Roden, Eric S. Boyd, David M. Ward, Satoshi Hanada, Donald A. Bryant
Publication title: Frontiers in Microbiology 9:3159, 2019

Abstract:
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
Full text link https://tinyurl.com/35vp44zb

Article title: Rotten thallus of Red Seaweed, Gracilariopsis heteroclada Zhang et Xia, is Associated with Agar-Digesting Bacillus spp
Authors: Joval N. Martinez and Philip Ian P. Padilla
Publication title: Journal of Fisheries Sciences, 2017

Abstract:
Agar-digesting bacteria have been hypothesized to cause rottening of the thalli of economically important marine red seaweeds, Gracilariopsis heteroclada Zhang et Xia (Gracilariaceae, Rhodophyta). However, characterization of these causative agents accompanying seaweeds’ disease in the marine environment has been poorly elucidated. Thus, agar-digesting bacteria associated with ‘rottening thallus’ of red seaweed, were isolated and characterized. Agar-digesters were selected based on their ability to digest agar by forming a clear depression around their colony and/or liquefaction of agar. Selected agar-digesters showed a positive result for gelatinase test and arginine dihydrolase test. 16S rRNA of these isolates was successfully extracted, purified, sequenced and analyzed. Phylogenetic analyses showed that bacterial 16S rRNA sequences from rottening seaweed thalli belong to Bacillus spp (98-99%), suggesting that the isolates were significantly associated with the rottening of red seaweeds in the present investigation.
Full text link https://tinyurl.com/y7v37cwt

Article title: Isolation and characterization of agar-digesting Vibrio species from the rotten thallus of Gracilariopsis heteroclada Zhang et Xia
Authors: Joval N. Martinez and Philip Ian P. Padilla
Publication title: Marine Environmental Research 119(1), 2016

Abstract:
Gracilariopsis heteroclada Zhang et Xia (Gracilariaceae, Rhodophyta) is one of the most studied marine seaweeds due to its economic importance. This has been cultivated extensively on commercial scale in the Philippines and other Asian countries. However, sustainable production of G. heteroclada in the Philippines could not be maximized due to the occurrence of rotten thallus disease. Thus, isolation and characterization of agar-digesting bacteria from the rotten thalli of G. heteroclada was conducted. A total of seven representative bacterial isolates were randomly selected based on their ability to digest agar as evidenced by the formation of depressions around the bacterial colonies on nutrient agar plates supplemented with 1.5% NaCl and liquefaction of agar. Gram-staining and biochemical characterization revealed that isolates tested were gram-negative rods and taxonomically identified as Vibrio parahaemolyticus (86–99.5%) and Vibrio alginolyticus (94.2–97.7%), respectively. It is yet to be confirmed whether these agar-digesting vibrios are involved in the induction and development of rotten thallus disease in G. heteroclada in concomitance with other opportunistic bacterial pathogens coupled with adverse environmental conditions.
Full text available upon request to the author/s.