Cultivation of Important Methanotrophs From Indian Rice Fields

Impact of Rhizospheric Microbiome on Rice Cultivation

The rhizosphere niche is extremely important for the overall growth and development of plants. Evidently, it is necessary to understand the complete mechanism of plant microbe interactions of the rhizosphere for sustainable and low input productivity. To meet the increasing global food demand, rice (Oryza sativa L.) agriculture seeks optimal conditions. The unique oxic-anoxic interface of rice-growing soil has invited divergent microbes with dynamic biogeochemical cycles. This review provides the systematic analysis of microbes associated with the major biogeochemical cycles with the aim to generate better management strategies of rhizospheric microbiome in the field of rice agriculture. For instance, several methanogenic and methanotrophic bacteria in the rice rhizosphere make an equilibrium for methane concentration in the environment. The carbon sequestration in paddy soil is again done through many rhizospheric microorganisms that can directly assimilate CO2 with their photoautotrophic mode of nutrition. Also the phosphate solubilizing microbes remain to be the most important keys for the PGPR activity of the paddy ecosystem. In addition, rhizospheric microbiome remain crucial in degradation and solubilization of organo-sulfur and insoluble inorganic sulfides which can be taken by the plants. Further, this review elucidates on the advantages of using metagenomic and metaproteomic approaches as an alternative of traditional approaches to understand the overall metabolic pathways operational in paddy-field. These knowledges are expected to open new possibilities for designing the balanced microbiome used as inoculum for intensive farming and will eventually lead to exert positive impacts on rice cultivation.

Diverse type I and type II methanotrophs cultivated from an Indian freshwater wetland habitat

Wetlands are the main natural sources of methane emissions, which make up a significant portion of greenhouse gas emissions. Such wetland patches serve as rich habitats for aerobic methanotrophs. Limited knowledge of methanotrophs from tropical wetlands widens the scope of study from these habitats. In the present study, a freshwater wetland in a tropical region in India was sampled and serially diluted to obtain methanotrophs in culture. This was followed by the isolation of methanotrophs on agarose-containing plates, incubated under methane: air atmosphere. Methanotrophs are difficult to cultivate, and very few cultures of methanotrophs are available from tropical wetlands. Our current study reports the cultivation of a diverse community of methanotrophs from six genera, namely, Methylomonas, Methylococcus, Methylomagnum, Methylocucumis (type I methanotrophs) along with Methylocystis, Methylosinus (type II methanotrophs). A high abundance of methanotrophs (106-1010 methanotrophs/g fresh weight) was observed in the samples. A Methylococcus strain could represent a putative novel species that was also isolated. Cultures of Methylomagnum and Methylocucumis, two newly described type I methanotrophs exclusively found in rice fields, were obtained. A large number of Methylomonas koyamae strains were cultured. Our study is pioneering in the documentation of culturable methanotrophs from a typical tropical wetland patch. The isolated methanotrophs can act as models for studying methanotroph-based methane mitigation from wetland habitats and can be used for various mitigation and valorization applications.

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.

Untapped talents: insight into the ecological significance of methanotrophs and its prospects

The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.

Methylococcus mesophilus sp. nov., the first non-thermotolerant methanotroph of the genus Methylococcus, from a rice field

Strain 16-5T, a mesophilic methanotroph of the genus Methylococcus, was isolated from rice field soil sampled in Chungcheong Province, Republic of Korea. Strain 16-5T had both particulate and soluble methane monooxygenases and could only grow on methane and methanol as electron donors. Strain 16-5 T cells are Gram-negative, white to light tan in color, non-motile, non-flagellated, diplococcoid to cocci, and have the typical type I intracytoplasmic membrane system. Strain 16-5T grew at 18-38 °C (optimum, 27 °C) and at pH 5.0-8.0 (optimum, pH 6.5-7.0). C16 : 1 ω7c (38.8%), C16 : 1  ω5c (18.8%), C16 : 1  ω6c (16.8%) and C16 : 0 (16.9%) were the major fatty acids, and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid were the major polar lipids. The main respiratory quinone was methylene-ubiquinone-8. Strain 16-5T displayed the highest 16S rRNA gene sequence similarities to other taxonomically recognized members of the genus Methylococcus, i.e. Methylococcus capsulatus TexasT (98.62%) and Methylococcus geothermalis IM1T (98.49 %), which were its closest relatives. It did, however, differ from all other taxonomically described Methylococcus species due to some phenotypic differences, most notably its inability to grow at temperatures above 38 °C, where other Methylococcus species thrive. Its 4.34 Mbp-sized genome has a DNA G+C content of 62.47 mol%, and multiple genome-based properties such as average nucleotide identity and digital DNA-DNA hybridization value distanced it from its closest relatives. Based on the data presented above, this strain represents the first non-thermotolerant species of the genus Methylococcus. The name Methylococcus mesophilus sp. nov. is proposed, and 16-5T (=JCM 35359T=KCTC 82050T) is the type strain.

Thermotolerant methanotrophs belonging to the Methylocaldum genus dominate the methanotroph communities in biogas slurry and cattle dung: A culture-based study from India

Biogas reactors run on various types of waste, with cattle dung and agricultural wastes being the primary sources in India. As biogas contains 50-60% methane, there is a possibility that the reactors harbour methanotrophs or methane-oxidizing bacteria. We set up serial endpoint dilution enrichments for the cultivation of methanotrophs using slurry from a small biogas reactor and cattle dung samples and obtained cultures of Methylocaldum gracile, a thermotolerant methanotroph. The study was expanded by sampling reactors of another small reactor of 20 L capacity and two 1000 L reactors. Dung samples were obtained from two Indian cattle breeds (Tharparkar and Gir). Pulverized rice straw used for feeding the biogas was also used for experiments. All the enrichment bottles were incubated at 39 °C, the reactors' in-situ temperature, and the rumen gut temperature. Our study isolated four pure cultures most related to Methylocaldum gracile VKM-14L^T, two strains from cattle dung samples, and two from reactors. The study also resulted in the cultivation of four additional cultures of Methylocaldum gracile and Methylocaldum tepidum, which were non-axenic and identified by pmoA gene sequencing. Pure cultures Methylocaldum gracile RS-9 and CDP-2 were studied for optimum temperature and oxygen. Both the strains were thermotolerant and grew in the temperature range of 25-45 °C with the optimum between 37 and 45 °C. The cultures could grow with minimal oxygen (0.5%-1%) in the headspace, with growth up to 10% oxygen. To summarize, we report the cultivation and isolation of methanotrophs from biogas slurries and cattle dung samples. Methylocaldum was the dominant methanotroph cultured, probably due to its thermotolerant nature and the ability to grow under variable oxygen conditions. The present study also expands the existing knowledge about habitats known for the genus Methylocaldum. An analysis of the isolated cultures would help us design strategies for methane mitigation from ruminants.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.