Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane

Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.

Complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment

We report the complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment in Singapore. The genome contains genes involved in methane, methanol, formaldehyde, and formate oxidation. It also contains genes utilizing various nitrogen sources such as nitrogen, nitrate, nitrite, urea, and ammonium.

Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook

Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.

Spatial-temporal variability of microphytoplankton assemblages including harmful microalgae in a tropical semi-enclosed strait (Johor Strait, Malaysia)

Harmful algal blooms (HABs) were not new to the tropical semi-enclosed Johor Strait, with incident records that could trace back to the 1980s. HAB monitoring in the area, often, is reactive, focusing only on HAB taxa previously causing problems but neglecting potential emerging HABs. To develop datasets on HABs that can better inform and improve management practices, monitoring should expand to sample whole microphytoplankton communities. In this study, microphytoplankton community structure across the Strait was investigated. Abundances of microphytoplankton and a suite of in situ water parameters of temperatures, salinity, pH, dissolved oxygen levels, macronutrients, and chlorophyll-a contents were collected at ten sites across the Strait at monthly intervals from January 2017 to December 2018. A total of 48 genera (51 taxa) microphytoplankton were identified microscopically. Diatom was the most diverse group (32 genera), followed by dinophyte (15 genera). Bloom-forming species included diatoms Chaetoceros, Coscinodiscus, Eucampia, Pseudo-nitzschia, Rhizosolenia, Skeletonema, Thalassiosira, and dinophytes Blixaea quinquecornis and Scrippsiella. Diatom taxa that exhibit high in situ growth rates were predominant in the low-nutrient marine-influenced environment. Bloom-forming taxa including HAB taxa were found dominant in the environment with high nutrient levels and mesohaline, salinity-stratified conditions. This study provides valuable baseline data that could assist in monitoring and prediction of HABs in the Johor Strait and could be of reference to other similar tropical coastal systems.

Prolonged high biomass diatom blooms induced formation of hypoxic-anoxic zones in the inner part of Johor Strait

The Johor Strait has experienced rapid development of various human activities and served as the main marine aquaculture area for the two countries that bordered the strait. Several fish kill incidents in 2014 and 2015 have been confirmed, attributed to the algal blooms of ichthyotoxic dinoflagellates; however, the cause of fish kill events after 2016 was not clarified and the causative organisms remained unknown. To clarify the potential cause of fish kills along the Johor Strait, a 1-year field investigation was conducted with monthly sampling between May 2018 and April 2019. Monthly vertical profiles of physical water parameters (temperature, salinity, and dissolved oxygen levels) were measured in situ at different depths (subsurface, 1 m, 5 m, and 8 m) depending on the ambient depth of the water column at the sampling stations. The spatial-temporal variability of macronutrients and chlorophyll a content was analyzed. Our results showed that high chlorophyll a concentration (up to 48.8 μg/L) and high biomass blooms of Skeletonema, Chaetoceros, Rhizosolenia, and Thalassiosira were observed seasonally at the inner part of the strait. A hypoxic to anoxic dead zone, with the dissolved oxygen levels ranging from 0.19 to 1.7 mg/L, was identified in the inner Johor Strait, covering an estimated area of 10.3 km². The occurrence of high biomass diatom blooms and formation of the hypoxic-anoxic zone along the inner part Johor Strait were likely the culprits of some fish kill incidents after 2016.

Comprehensive in silico modeling of the rice plant PRR Xa21 and its interaction with RaxX21-sY and OsSERK2

The first layer of defense that plants deploy to ward off a microbial invasion comes in the form of pattern-triggered immunity (PTI), which is initiated when the pattern-recognition receptors (PRRs) bind with the pathogen-associated molecular patterns (PAMPs) and co-receptor proteins, and transmit a defense signal. Although several plant PRRs have been discovered, very few of them have been fully characterized, and their functional parameters assessed. In this study, the 3D-model prediction of an entire plant PRR protein, Xa21, was done by implementing multiple in silico modeling techniques. Subsequently, the PAMP RaxX21-sY (sulphated RaxX21) and leucine-rich repeat (LRR) domain of the co-receptor OsSERK2 were docked with the LRR domain of Xa21. The docked complex of these three proteins formed a heterodimer that closely resembles the other crystallographic PTI complexes available. Molecular dynamics simulations and MM/PBSA calculations were applied for an in-depth analysis of the interactions between Xa21 LRR, RaxX21-sY, and OsSERK2 LRR. Arg230 and Arg185 from Xa21 LRR, Val2 and Lys15 from RaxX21-sY and Lys164 from OsSERK2 LRR were found to be the prominent residues which might contribute significantly in the formation of a heterodimer during the PTI process mediated by Xa21. Additionally, RaxX21-sY interacted much more favorably with Xa21 LRR in the presence of OsSERK2 LRR in the complex, which substantiates the necessity of the co-receptor in Xa21 mediated PTI to recognize the PAMP RaxX21-sY. However, the free energy binding calculation reveals the favorability of a heterodimer formation of PRR Xa21 and co-receptor OsSERK2 without the presence of PAMP RaxX21-sY, which validate the previous lab result.

Microbiological analysis of drinking water from water vending machines

Commercial water vending machines are gaining popularity nowadays among the general public, probably due to the ease of obtaining clean drinking water. However, improper maintenance of the machines can lead to bacterial contamination. Hence, this study aimed to investigate and determine the microbiological characteristics of drinking water from Water Vending Machines (WVM) by isolating and characterizing culturable bacteria in the water and nozzle swab samples. The samples were obtained from WVM at eight different locations around Johor Bahru, Johor, Malaysia. Several unique bacterial isolates were found, from both Gram-positive and Gram-negative groups. Polymerase chain reaction amplification and 16S rRNA sequence analysis suggested that these isolates are from Pseudomonas, Bacillus, and Stenotrophomonas genera. In situ water quality tests which include pH, conductivity, and total dissolved solids were also conducted. Two samples from the inlet source have pH and conductivity values slightly above the reference values stipulated in drinking water regulations. The findings presented here suggest the importance of regular service maintenance of the WVM to ensure that the water samples meet the standard stipulated by the authority.

Biohydrogen Production by Antarctic Psychrotolerant Klebsiella sp. ABZ11

Lower temperature biohydrogen production has always been attractive, due to the lower energy requirements. However, the slow metabolic rate of psychrotolerant biohydrogen-producing bacteria is a common problem that affects their biohydrogen yield. This study reports on the improved substrate synthesis and biohydrogen productivity by the psychrotolerant Klebsiella sp. strain ABZ11, isolated from Antarctic seawater sample. The isolate was screened for biohydrogen production at 30°C, under facultative anaerobic condition. The isolate is able to ferment glucose, fructose and sucrose with biohydrogen production rate and yield of 0.8 mol/l/h and 3.8 mol/g, respectively at 10 g/l glucose concentration. It also showed 74% carbohydrate uptake and 95% oxygen uptake ability, and a wide growth temperature range with optimum at 37°C. Klebsiella sp. ABZ11 has a short biohydrogen production lag phase, fast substrate uptake and is able to tolerate the presence of oxygen in the culture medium. Thus, the isolate has a potential to be used for lower temperature biohydrogen production process.

Reduction of azo dyes by flavin reductase from Citrobacter freundii A1

<em>Citrobacter freundii </em>A1 isolated from a sewage treatment facility was demonstrated to be able to effectively decolorize azo dyes as pure and mixed culture. This study reports on the investigation on the enzymatic systems involved. An assay performed suggested the possible involvement of flavin reductase (Fre) as an azo reductase. A heterologouslyexpressed recombinant Fre from <em>C. freundii </em>A1 was used to investigate its involvement in the azo reduction process. Three model dyes were used, namely Acid Red 27 (AR27), Direct Blue 15 (DB15) and Reactive Black 5 (RB5). AR27 was found to be reduced the fastest by Fre, followed by RB5, and lastly DB15. Redox mediators nicotinamide adenine dinucleotide (NADH) and riboflavin enhance the reduction, suggesting the redox activity of the enzyme. The rate and extent of reduction of the model dyes correlate well with the reduction potentials (<em>E</em>_p). The data presented here strongly suggest that Fre is one of the enzymes responsible for azo reduction in <em>C. freundii </em>A1, acting via an oxidation-reduction reaction.

The pH sensitivity of murine heat shock protein 47 (HSP47) binding to collagen is affected by mutations in the breach histidine cluster

Heat shock protein 47 (HSP47) is a single-substrate molecular chaperone crucial for collagen biosynthesis. Although its function is well established, the molecular mechanisms that govern binding to procollagen peptides and triple helices in the endoplasmic reticulum (followed by controlled release in the Golgi) are unclear. HSP47 binds procollagen at a neutral pH but releases at a pH similar to the pK(a) of the imidazole side chain of histidine residues. It thus seems likely that these residues are involved in this pH-dependent mechanism. Murine HSP47 has 14 histidine residues grouped into three clusters, known as the breach, gate, and shutter. Here, we report the use of histidine mutagenesis to demonstrate the relative contribution of these three clusters to HSP47 structure and the "pH switch." Many of the tested mutants are silent; however, breach mutants H197A and H198A show binding but no apparent pH switch and are unable to control release. Another breach mutant, H191A, shows perturbed collagen release characteristics, consistent with observed perturbations in pH-driven trans-conformational changes. Thus, His-198, His-197 and His-191 are important (if not central) to HSP47 mechanism of binding/release to collagen. This is consistent with the breach cluster residues being well conserved across the HSP47 family.