Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.

Source or sink? A study on the methane flux from mangroves stems in Zhangjiang estuary, southeast coast of China

Mangrove ecosystems are an important component of "blue carbon". However, it is not clear whether the stems play roles in the CH₄ budget of mangrove ecosystems. This study investigated the CH₄ emission from mangrove stems and its potential driving factors. We set up six sample plots in the Zhangjiang Estuary National Mangrove Nature Reserve, where Kandelia obovata, Avicennia marina and Aegiceras corniculata are the main mangrove tree species. Soil properties such as total carbon content, redox potential and salinity were determined in each plot. The dynamic chamber method was used to measure mangrove stems and soil CH₄ fluxes. Combined field survey results with Principal Component Analysis (PCA) of soil properties, we divided the six plots into two sites (S1 and S2) to perform statistical analyses of stem CH₄ fluxes. Then the CH₄ fluxes from mangrove tree stems and soil were further scaled up to the ecosystem level through the mapping model. Under different backgrounds of soil properties, salinity and microbial biomass carbon were the main factors modified soil CH₄ fluxes in the two sites, and further affected the stem CH₄ fluxes of mangroves. The soil of both sites are sources of CH₄, and the soil CH₄ emission of S2 was about twice higher than that of S1. Results of upscaling model showed that mangrove stems in S1 were CH₄ sinks with -105.65 g d^-1. But stems in S2 were CH₄ sources around 1448.24 g d^-1. Taken together, our results suggested that CH₄ emission from mangrove soils closely depends on soils properties. And mangrove stems were found to act as both CH₄ sources and CH₄ sinks depend on soil CH₄ production. Therefore, when calculating the CH₄ budget of the mangrove ecosystem, the contribution of mangrove plant stems cannot be ignored.

Physiology of Methylotrophs Living in the Phyllosphere

Methanol is abundant in the phyllosphere, the surface of the above-ground parts of plants, and its concentration oscillates diurnally. The phyllosphere is one of the major habitats for a group of microorganisms, the so-called methylotrophs, that utilize one-carbon (C1) compounds, such as methanol and methane, as their sole source of carbon and energy. Among phyllospheric microorganisms, methanol-utilizing methylotrophic bacteria, known as pink-pigmented facultative methylotrophs (PPFMs), are the dominant colonizers of the phyllosphere, and some of them have recently been shown to have the ability to promote plant growth and increase crop yield. In addition to PPFMs, methanol-utilizing yeasts can proliferate and survive in the phyllosphere by using unique molecular and cellular mechanisms to adapt to the stressful phyllosphere environment. This review describes our current understanding of the physiology of methylotrophic bacteria and yeasts living in the phyllosphere where they are exposed to diurnal cycles of environmental conditions.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters

Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO₂/H₂). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH₄ L⁻¹ d⁻¹) was highest in the culture grown with tryptone, yeast extract, and CO₂/H_2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.

The Study on the Cultivable Microbiome of the Aquatic Fern Azolla Filiculoides L. as New Source of Beneficial Microorganisms

The aim of the study was to determine the still not completely described microbiome associated with the aquatic fern Azolla filiculoides. During the experiment, 58 microbial isolates (43 epiphytes and 15 endophytes) with different morphologies were obtained. We successfully identified 85% of microorganisms and assigned them to 9 bacterial genera: Achromobacter, Bacillus, Microbacterium, Delftia, Agrobacterium, and Alcaligenes (epiphytes) as well as Bacillus, Staphylococcus, Micrococcus, and Acinetobacter (endophytes). We also studied an A. filiculoides cyanobiont originally classified as Anabaena azollae; however, the analysis of its morphological traits suggests that this should be renamed as Trichormus azollae. Finally, the potential of the representatives of the identified microbial genera to synthesize plant growth-promoting substances such as indole-3-acetic acid (IAA), cellulase and protease enzymes, siderophores and phosphorus (P) and their potential of utilization thereof were checked. Delftia sp. AzoEpi7 was the only one from all the identified genera exhibiting the ability to synthesize all the studied growth promoters; thus, it was recommended as the most beneficial bacteria in the studied microbiome. The other three potentially advantageous isolates (Micrococcus sp. AzoEndo14, Agrobacterium sp. AzoEpi25 and Bacillus sp. AzoEndo3) displayed 5 parameters: IAA (excluding Bacillus sp. AzoEndo3), cellulase, protease, siderophores (excluding Micrococcus sp. AzoEndo14), as well as mineralization and solubilization of P (excluding Agrobacterium sp. AzoEpi25).