Unraveling the impact of lanthanum on methane consuming microbial communities in rice field soils

The discovery of the lanthanide requiring enzymes in microbes was a significant scientific discovery that opened a whole new avenue of biotechnological research of this important group of metals. However, the ecological impact of lanthanides on microbial communities utilizing methane (CH4) remains largely unexplored. In this study, a laboratory microcosm model experiment was performed using rice field soils with different pH origins (5.76, 7.2, and 8.36) and different concentrations of La3+ in the form of lanthanum chloride (LaCl3). Results clearly showed that CH4 consumption was inhibited by the addition of La3+ but that the response depended on the soil origin and pH. 16S rRNA gene sequencing revealed the genus Methylobacter, Methylosarcina, and Methylocystis as key players in CH4 consumption under La3+ addition. We suggest that the soil microbiome involved in CH4 consumption can generally tolerate addition of high concentrations of La3+, and adjustments in community composition ensured ecosystem functionality over time. As La3+ concentrations increase, the way that the soil microbiome reacts may not only differ within the same environment but also vary when comparing different environments, underscoring the need for further research into this subject.

Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.

Soil aeration rather than methanotrophic community drives methane uptake under drought in a subtropical forest

Little information is available about the effects of drought on soil methane (CH₄) uptake and the underlying feedback of the soil microbial community in forest biomes. More importantly, a meta-analysis of the current literature on this topic revealed that there are virtually no data available in subtropical forests. To fill the abovementioned knowledge gap, we carried out a 3-year investigation of in situ CH₄ efflux under drought in a subtropical forest, and found that drought significantly increased soil CH₄ uptake (P < 0.001). However, drought did not change oxidation potentials and abundances of methanotrophs, and similar methanotrophic communities were observed between the drought and ambient control sites based on metagenomic sequencing analysis. Active methanotrophic communities were dominated by the genus Methylosinus based on DNA stable-isotope probing analysis. Structural equation model analysis indicated that direct drought-derived pathway, i.e., increasing soil aerations, outweighs the indirect pathway, i.e., altering methanotrophic communities and activities, and plays a predominant role in driving soil CH₄ uptake in forest ecosystems. To our knowledge, our work is the first study to investigate the effects of drought on in situ CH₄ efflux and the underlying microbial mechanisms in subtropical forests.

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities

DNA modification techniques are increasingly applied to improve the agronomic performance of crops worldwide. Before cultivation and marketing, the environmental risks of such modified varieties must be assessed. This includes an understanding of their effects on soil microorganisms and associated ecosystem services. This study analyzed the impact of a cisgenic modification of the potato variety Desirée to enhance resistance against the late blight-causing fungus Phytophthora infestans (Oomycetes) on the abundance and diversity of rhizosphere inhabiting microbial communities. Two experimental field sites in Ireland and the Netherlands were selected, and for 2 subsequent years, the cisgenic version of Desirée was compared in the presence and absence of fungicides to its non-engineered late blight-sensitive counterpart and a conventionally bred late blight-resistant variety. At the flowering stage, total DNA was extracted from the potato rhizosphere and subjected to PCR for quantifying and sequencing bacterial 16S rRNA genes, fungal internal transcribed spacer (ITS) sequences, and nir genes encoding for bacterial nitrite reductases. Both bacterial and fungal communities responded to field conditions, potato varieties, year of cultivation, and bacteria sporadically also to fungicide treatments. At the Dutch site, without annual replication, fungicides stimulated nirK abundance for all potatoes, but with significance only for cisgenic Desirée. In all other cases, neither the abundance nor the diversity of any microbial marker differed between both Desirée versions. Overall, the study demonstrates environmental variation but also similar patterns of soil microbial diversity in potato rhizospheres and indicates that the cisgenic modification had no tangible impact on soil microbial communities.

A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency.