Methane Turnover in Desert Soils

Deserts cover about a third of the land surface on Earth. However, despite their size, their ecology – and particularly their microbial ecology – is far less understood than the ecology of more humid regions. Previous studies have indicated that desert soils might be involved in the production and consumption of methane, an important greenhouse gas. The turnover of atmospheric gases involves many microorganisms, and methane is no exception – it is both produced and consumed by microbes. Despite the extensive research methane has been subjected to, a rigorous study striving to elucidate methane turnover patterns in arid regions and aiming to detect the active organisms involved has not been conducted so far. This work comprises three parts. The first part deals with biogeographical patterns of soil microbial communities along a steep rainfall gradient in Israel ranging from less than 100 to more than 900 mm yr-1. We show that community profiles of both Archaea and Bacteria do not change continuously along the gradient, but rather cluster into three groups that we have defined as arid, semi-arid and Mediterranean. These three categories demonstrate a qualitative difference in the microbiology of arid soil compared to more humid regions. In the second part we show that pristine arid soils in the Negev Desert, Israel, are sinks for atmospheric methane, but that disturbed sites and pristine hyper-arid sites are probably not. The methanotrophic activity was located in a narrow layer in the soil down to about 20 cm depth. Interestingly, the biological soil crust (BSC) which is typically the most active layer in desert soils showed no methane uptake activity and was apparently devoid of methanotrophs. Transcripts of the key methanotrophic gene – encoding for the particulate methane monooxygenase (PMMO) – were detected in the active soils and their sequences showed that they are affiliated with two clusters of uncultured methanotrophs: USC and JR3. Based on a correlation of the relative abundance of each methanotroph to the methane oxidation rate we concluded that JR3 is the dominant atmospheric methane oxidizer in this arid system. The third part deals with methanogenesis in upland soils with a focus on drylands. Following previous work we show that many upland soils, sampled globally, possess a methanogenic potential, when incubated anoxically, despite being aerated most of the time. Only two active methanogens were detected – Methanosarcina and Methanocella – which appear to be universal upland soil methanogens. Under these conditions, acetoclastic methanogenesis, mediated by Methanosarcina, was the dominant methanogenic pathway and cell numbers of Methanosarcina were well correlated with methane production rates. Lastly, we show that the BSC was the source for methanogenic activity in arid soils while the deeper layers showed little or no methanogenic potential. When the BSC was incubated in a wet state in microcosms and in the presence of oxygen methanogens could still grow and methane was still produced albeit at relatively low amounts. Both methanogens expressed the gene encoding for the oxygen detoxifying enzyme catalase giving at least some explanation to their ability to remain viable in the presence of oxygen. Under these conditions, Methanocella was the dominant methanogen and most methane was produced from H2/CO2, indicating niche differentiation between the two methanogens. The findings of this work suggest that under standard dry conditions pristine arid soils are a net sink for atmospheric methane but that following a rain event they might turn into net sources

Biotic interactions in microbial communities as modulators of biogeochemical processes : methanotrophy as a model system

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes

Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities

Amplified ribosomal DNA restriction analysis (ARDRA) and restriction fragment length polymorphism were originally used for strain typing and for screening clone libraries to identify phylogenetic clusters within a microbial community. Here we used ARDRA as a model to examine the capacity of restriction-based techniques for clone identification, and the possibility of deriving phylogenetic information from ARDRA-based dendrograms. ARDRA was performed in silico on 48,759 sequences from the Ribosomal Database Project, and it was found that the fragmentation profiles were not necessarily unique for each sequence in the database, resulting in different species sharing fragmentation profiles. Although ARDRA-based clusters separated clones into different genera, these phylogenetic clusters did not overlap with trees constructed according to sequence alignment, calling into question the intra-genus ARDRA-based phylogeny. It is thus suggested that the prediction power of ARDRA clusters in identifying clone phylogeny be regarded with caution

Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen

Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ13C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H2/CO2 under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle

roey-angel/Rock_weathering: First release - for preprint

Release 1.0.0 for submitting a discussion paper to Biogeoscience

Methane Turnover in Desert Soils

Deserts cover about a third of the land surface on Earth. However, despite their size, their ecology – and particularly their microbial ecology – is far less understood than the ecology of more humid regions. Previous studies have indicated that desert soils might be involved in the production and consumption of methane, an important greenhouse gas. The turnover of atmospheric gases involves many microorganisms, and methane is no exception – it is both produced and consumed by microbes. Despite the extensive research methane has been subjected to, a rigorous study striving to elucidate methane turnover patterns in arid regions and aiming to detect the active organisms involved has not been conducted so far. This work comprises three parts. The first part deals with biogeographical patterns of soil microbial communities along a steep rainfall gradient in Israel ranging from less than 100 to more than 900 mm yr-1. We show that community profiles of both Archaea and Bacteria do not change continuously along the gradient, but rather cluster into three groups that we have defined as arid, semi-arid and Mediterranean. These three categories demonstrate a qualitative difference in the microbiology of arid soil compared to more humid regions. In the second part we show that pristine arid soils in the Negev Desert, Israel, are sinks for atmospheric methane, but that disturbed sites and pristine hyper-arid sites are probably not. The methanotrophic activity was located in a narrow layer in the soil down to about 20 cm depth. Interestingly, the biological soil crust (BSC) which is typically the most active layer in desert soils showed no methane uptake activity and was apparently devoid of methanotrophs. Transcripts of the key methanotrophic gene – encoding for the particulate methane monooxygenase (PMMO) – were detected in the active soils and their sequences showed that they are affiliated with two clusters of uncultured methanotrophs: USC and JR3. Based on a correlation of the relative abundance of each methanotroph to the methane oxidation rate we concluded that JR3 is the dominant atmospheric methane oxidizer in this arid system. The third part deals with methanogenesis in upland soils with a focus on drylands. Following previous work we show that many upland soils, sampled globally, possess a methanogenic potential, when incubated anoxically, despite being aerated most of the time. Only two active methanogens were detected – Methanosarcina and Methanocella – which appear to be universal upland soil methanogens. Under these conditions, acetoclastic methanogenesis, mediated by Methanosarcina, was the dominant methanogenic pathway and cell numbers of Methanosarcina were well correlated with methane production rates. Lastly, we show that the BSC was the source for methanogenic activity in arid soils while the deeper layers showed little or no methanogenic potential. When the BSC was incubated in a wet state in microcosms and in the presence of oxygen methanogens could still grow and methane was still produced albeit at relatively low amounts. Both methanogens expressed the gene encoding for the oxygen detoxifying enzyme catalase giving at least some explanation to their ability to remain viable in the presence of oxygen. Under these conditions, Methanocella was the dominant methanogen and most methane was produced from H2/CO2, indicating niche differentiation between the two methanogens. The findings of this work suggest that under standard dry conditions pristine arid soils are a net sink for atmospheric methane but that following a rain event they might turn into net sources

Co-assembled metatranscriptomic reads from the hindgut samples from the millipede species, Glomeris connexa

Three quality-filtered reads from the hindgut samples of Glomeris connexa were co-assembled (de novo) with Trinity v2.13.2.</p

Co-assembled metatranscriptomic reads from the hindgut samples from the millipede species, Epibolus pulchripes

Three quality-filtered reads from the hindgut samples of Epibolus pulchripes were co-assembled (de novo) with Trinity v2.13.2. </p

The origin and role of biological rock crusts in rocky desert weathering

In drylands, microbes that colonise rock surfaces were linked to erosion because water scarcity excludes traditional weathering mechanisms. We studied the origin and role of rock biofilms in geomorphic processes of hard lime and dolomitic rocks that feature comparable weathering morphologies though originating from arid and hyperarid environments, respectively. We hypothesised that weathering patterns are fashioned by salt erosion and mediated by the rock biofilms that originate from the adjacent soil and dust. We used a combination of microbial and geological techniques to characterise rocks morphologies and the origin and diversity of their biofilm. Amplicon sequencing of the SSU rRNA gene suggested that bacterial diversity is low and dominated by Proteobacteria and Actinobacteria. These phyla formed laminar biofilms only on rock surfaces that were exposed to the atmosphere and burrowed up to 6 mm beneath the surface, protected by sedimentary deposits. Unexpectedly, the microbial composition of the biofilms differed between the two rock types and was also distinct from the communities identified in the adjacent soil and settled dust, showing a habitat-specific filtering effect. Moreover, the rock bacterial communities were shown to secrete extracellular polymeric substances that form an evaporation barrier, reducing water loss rates by 65-75%. The reduced water transport rates through the rock also limit salt transport and its crystallisation in surface pores, which is thought to be the main force for weathering. Concomitantly, the biofilm layer stabilises the rock surface via coating and protects the weathered front. Our hypothesis contradicts common models, which typically consider biofilms as weathering-promoting agents. In contrast, we propose the microbial colonisation of mineral surfaces acts to mitigate geomorphic processes in hot, arid environments

Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy

Abstract Background Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics. Results The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet. Conclusions Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstrac