Environmental Microbiology



Environmental microbiology is the study of microorganisms that inhabit the Earth and their roles in carrying out processes in both natural and human-made systems; emphasis is on the interfaces between environmental sciences andmicrobial diversity, including microbial processes in the environment, microbial communities and microbial interactions. Mangrove area or coastal area is one of the unique environments owing to their fluctuating nature in temperature, pH, salinity, sea surface temperature, current, precipitation regime and wind pattern.

Accordingly, this environment maintains complicated microbial communities and possesses abundant resource for novel microorganisms and secondary metabolites. Our scope focuses on the isolation and characterization of microorganisms, mainly from mangrove and marine environments, to search for novel bacterial species, useful enzymes and secondary metabolites. Currently, five members are involved in this project, including Prof. Amirul Al-Ashraf, Dr. Go Furusawa, Dr. Ira Aryani, Ms. Amrina Rosyada as well as Mrs. Azura. 

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Identification of novel bacteria isolated from mangrove soil

Mangrove sediment represents one of the most dynamic and diverse microbial habitats. Malaysian mangrove is the third largest mangrove in the Asia-Pacific region. However, microbial studies on Malaysian mangrove are still scarce. Accordingly, our group performed to isolate bacteria from mangrove sediment, mainly the Matang mangrove forest, Perak, Malaysia. Currently, we have isolated more than 250 strains and have found several candidates of new genus and species, as follows:

1. Mangrovimonas xylaniphaga ST2L12TThe 16S rRNA gene sequence of this strain showed 95.3% similarity to Mangrovimonas yuxiaonensis. ST2L12T exhibited degradation of xylan, casein and tween 80 while M. yuxiaonensis did not show the phenotypes.

2. Microbulbifer aggregans CCB-MM1TThe 16S rRNA gene sequence of this strain showed 98.12 %, 97.46 % and 97.33 % similarity with M. rhizosphaerae, M. maritimus and M. gwangyangensis, respectively. Interestingly, only this strain showed cell aggregation in stationary phase.

In addition, we are performing the characterization of new Catenovulum-like bacterium and Hahella sp.

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Mechanism of bacterial predation in Aureispira sp. CCB-QB1

Aureispira sp. CCB-QB1 is a bacterial predator in the marine environment. This strain can capture and prey on bacteria cells such as Vibrio sp. in the presence of calcium ion. Calcium ion may help to neutralize the electrical forces of the cell surface that cause repulsion between cells. As a result, the cells in the presence of calcium ion can form aggregates and capture its prey. This mechanism may be useful for removing organic compounds or heavy metals from waste solution.      









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A diauxic growth of marine agarolytic bacterium Persicobacter sp. CCB-QB2

Diauxic growth is a two-phase growth response seen in the presence of two different substrates and is mainly observed in gut microbes. However, marine agarolytic bacterium Persicobacter sp. CCB-QB2 also exhibits diauxic growth in the presence of nitrogen source and agar in culture medium. Additionally, QB2 cells strongly produce agar degradation enzymes in the second growth phase. The diauxic growth may play an important role in the production of carbohydrate degradation enzymes, such as agarase, in marine bacteria.

A novel thermostable and detergent-tolerant β-agarase from Persicobacter sp. CCB-QB2

Agarolytic bacterium, Persicobacter sp. CCB-QB2 produced four agarolytic enzymes. One of them, PdAgaC, exhibited unique characters. PdAgaC showed thermostability at 50 °C and tolerance towards several detergents. In addition, the activity of PdAgaC after incubation with 0.1% of SDS and Triton X-100 increased approximately 1.2-fold. The agarolytic activity was outstandingly higher than that of many known agrases.

Generally, β-agarases produce neoagarobiose (dimer), neoagarotetraose (tetramer) and neoagarohexaose (hexamer) as its hydrolyzate, not monomeric sugar. Interestingly, although the major hydrolytic product of PdAgaC was neoagarobiose, monomeric sugar was also produced. This is the first report of an agarase which can produce monomeric sugar from agarose.

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A rod-coccus cell cycle of the genus Microbulbifer

Some bacteria reduce their cell size upon carbon starvation. This phenomenon is called as a rod-coccus cell cycle. The cell cycle is regulated by the bolA gene that encodes a DNA-binding protein. Microbulbifer sp. CCB-MM1 strain, isolated from mangrove sediment, also shows a rod-coccus cell cycle and additionally forms aggregates in starvation condition.

An experiment of qRT-PCR gene expression revealed that the cycle of MM1 strain was not regulated by the bolA gene, indicating MM1 may have alternative pathways. Now, we are performing whole-transcriptomic analysis to search for genes related to the cell cycle in MM1 strain.






















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Screening of potential secondary metabolites

Bacteria, particularly actinomycetes, are great producers of bioactive compounds. In CCB, we have a culture collection known as Microbial Biodiversity Library (MBL). Research conducted in this group includes various assays to screen the presence of potential secondary metabolites from those microbes, such as anti-infective, anti-oxidant, anti-microbial, plant growth promoters, siderophore production, etc.


Currently, a new potential anti-infective agent was successfully isolated and characterized from marine actinomycetes. Streptomyces sp. CCB-PSK 207 was found to rescue Caenorhabditis elegans from Pseudomonas aeruginosa infection through restitution of suppressed lysozyme 7 activities. A hexane partition of the extract from this isolate could promote the survival of PA14-infected worms to more than 60%. In addition, the partition was able to induce the expression of lysozyme 7, an important innate immunity defense molecule of C. elegans.


Besides the anti-infective agent, we have identified and characterized anti-oxidant bioactive metabolites from mangrove Streptomyces. These Streptomyces also showed good anti-microbial activities against several human pathogens. Various assays were performed, including phosphomolybdate assay, DPPH (1, 1, diphenyl-2-picryl hydrazyl) scavenging activity assay, reducing power assay, Beta-carotene bleaching disc diffusion assay, etc. Further elucidation of the bioactive compound structures is currently in progress.

Antimicrobial & plant growth promoters

Recently, agriculture has been faced with destructive activities caused by numerous pests, including microbial pathogens, weeds and insects, which resulted in drastic decrease of crop yield. Screening of new biopesticide agents, plant growth promoters, as well as siderophore producers, will be definitely improving our future agriculture. Based on primary studies, few potential Streptomyces have been characterized. These isolates show the ability of plant growth promoters as well as anti-phytopathogenic producers. Partitioning of the extract and characterization of the bioactive molecules will be conducted to elucidate the structure of the active compound.

Presently, we are also actively screening the secondary metabolites from MBL for other research purposes.











Crystal structure of a neoagarobiose-producing GH16 family β-agarase from Persicobacter sp. CCB-QB2
Teh, A.-H., Fazli, N.H., Furusawa, G.
(2020) Applied Microbiology and Biotechnology, 104 (2), pp. 633-641.


Complete Genome Sequence Of The Novel Agarolytic Catenovulum-Like Strain CCB-QB4 
Lau, N.-S., Tan, W.R., Furusawa, G., Amirul, A.-A.A. 
(2019) Marine Genomics, 43, pp. 50-53.

Biochemical Characterization of Thermostable and Detergent-Tolerant β-Agarase, PdAgaC, from Persicobacter sp. CCB-QB2
Hafizah, N.F., Teh, A.-H., Furusawa, G.
(2019) Applied Biochemistry and Biotechnology, 187 (3), pp. 770-781.

Draft genome sequence of the halophilic Pararhodobacter-like strain CCB-MM2, which has polyhydroxyalkanoate-synthesizing potential
Sam, K.-K., Lau, N.-S., Furusawa, G., Abdullah Amirul, A.-A.
(2019) Microbiology Resource Announcements, 8 (46), art. no. e01248-19,

Biodiversity of plant polysaccharide-degrading bacteria in mangrove ecosystem
Furusawa, G.
(2019) Tropical Life Sciences Research, 30 (3), pp. 157-172.



Metagenomic insights into the phylogenetic and functional profiles of soil microbiome from a managed mangrove in Malaysia 
Priya, G., Lau, N.-S., Furusawa, G., Dinesh, B., Foong, S.Y., Amirul, A.-A.A. 
(2018) Agri Gene, 9, pp. 5-15.

Modelling of polyhydroxyalkanoate synthase from Aquitalea sp. USM4 suggests a novel mechanism for polymer elongation
Teh, A.-H., Chiam, N.-C., Furusawa, G., Sudesh, K.
(2018) International Journal of Biological Macromolecules, 119, pp. 438-445.


Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2
Sim, P.-F., Furusawa, G., Teh, A.-H.
(2017), Scientific Reports, 7(1),13656

Draft genome sequence of halophilic Hahella sp. strain CCB-MM4, isolated from Matang Mangrove Forest in Perak, Malaysia
Ka-Kei Sam, Nyok Sean Lau, Go Furusawa, Al-Ashraf Abdullah Amirul.
(2017), Genome Announcements, 5(42),e01147-17

Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest
Moh, T.H., Furusawa, G., Amirul, A.A.-A.
(2017), nternational Journal of Systematic and Evolutionary Microbiology (2017), 67(10),002258, pp. 4089-4094.

Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia
Moh, T.H., Lau, N.-S., Furusawa, G., Amirul, A.-A.A.
(2017), Standards in Genomic Sciences (2017), 12(1),36

Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway
Go Furusawa, Nyok-Sean Lau, Suganthi Appalasamy, Amirul Al-Ashraf Abdullah.
(2017), Microbiology Open, doi: 10.1002/mbo3.405

Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of matang mangrove forest, malaysia
Balachandra Dinesh, Go Furusawa, A. A. Amirul. 2017.
(2017), Archives of Microbiology
, 199-63-67


Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes
Balachandra Dinesh, Nyok-Sean Lau, Go Furusawa, Seok-Won Kim, Todd D. Taylor, Swee Yeok Foong, Alexander Chong Shu-Chien.
(2016), Marine Genomics, 25 (2016), 115-121.

Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia
Dinesh B., Furusawa G., Amirul A.A.
(2016), Archives of Microbiology, 1-5