Genomic Adaptations and Physiology of Methanogens

Methane producing Archaea, i.e. methanogens, are nearly ubiquitous organisms in natural and engineered environments where anaerobic conditions and carbon degradation take place. Their ability to harvest energy at the low boundaries of thermodynamics and energetic yields, and their use of “waste” metabolites to produce CH4 allow: (i) their widespread presence, (ii) their key role in the last reducing steps of carbon decomposition, (iii) their diverse metabolic association with Bacteria, (iv) their functional diversity and complexity to exploit resources despite of high competition.

A key research area in the Cadillo Lab is to evaluate the physiology, metabolism and regulation of methanogens playing a key biogeochemical cycling role in OC degradation in C-rich wetlands, i.e. peatlands, and C-rich anaerobic bioreactors. We used genomics and complementary omics approaches to identify the genetic and physiological adaptations related to metabolism as well as maintenance of cell homeostasis, trophic interactions and long term evolutionary processes.

The following depicts two current efforts within this work:

A. Adaptations to Contrasting Peatlands

Contrasting peatlands, poor bogs vs rich fens, have dramatically different methanogenic community structures. Acidic bogs are dominated by a cluster previously called “E2”, representing between 55-99% of all Archaea; while circumneutral rich fens have more even communities co-dominated by three clades, representing a ~95% fraction, which includes the cluster previously called “E1”. Members of the cluster E2 and E1 are closely related (~94-96% 16S rRNA genetic ID) and are members of the novel family Methanoregulaceae. The fact that one is either dominant in acidic bogs or in circumneutral fens but less than 1% in their contrasting environment suggests their specialization to peatland type.

The main goals in this work are to evaluate whether novel methanogens acquired site-specific specializations at the genetic, regulatory or metabolic level and whether their metabolic interactions with Bacteria is regulated by adaptation to ecosystem type or to the phylogeny of a partner.

Methanoregula boonei and Methanosphaerula palustris, are novel isolates of the E2 and E1 cluster, respectively. Both organisms use H2/CO2 for methanogenesis, share mesophilic and sodium sensitivity traits, and also differ in key parameters such as pH response and growth rate. M. boonei lives in more acidic pHs (4.5-5.5) holding the most acidic optimal value (5.1) known for any methanogen; while M. palustris thrives under less acidic conditions (4.8-6.4) with optimal growth at mildly acidic pH (5.7). The mechanism of pH adaptation or basis for different doubling time (44 vs 19 hours in this case) for most methanogens is not known. The genomes of both strains were sequenced with the support of the DOE-JGI CSP program, and we have found several leads for novel adaptations relating to ion and cation transporters for cellular homeostasis. Also a significant part of their of genome resulted from horizontal acquisition from bacterial sources, and through comparative genomics we have also identified potential for differential metabolic functions of biosynthetic pathways.

This research attempts a system biology evaluation to identify adaptations and functional changes undertaken by methanogens in contrasting peatlands. Gene expression, protein and metabolite content are approaches being pursued.

Importantly, as part of our collaborative work, we have sequenced the genomes of two other members of the Methanoregulaceae family isolated from anaerobic bioreactors and we are currently developing and analysis to contrast “bioreactor” vs “peatland” methanogens. Diversity of hydrogenases and variable roles, is emerging as a possible key source of differentiation.

B. Adaptations to Contrasting Latitudes

In collaboration with faculty and staff researchers from the Join Genome Institute, the University of Illinois at Urbana-MethanogensChampaign and the National Institute of Advanced Industrial Science and Technology (Japan) we have sequenced the genomes of two novel strains (SWAN1, and AL-21), and four other species are under sequencing by our group. For this research we use a comparative genomic approach to evaluate the pangenome of member from this group focusing in isolates from Artic, Boreal, Temperate and Tropical wetlands. Unique physiological traits of “cold” methanobacteria versus “temperate” and “tropical” ones are among the focus of this research. Competition experiments will be followed up to quantify the fitness value of latitudinal adaptations in methanogenic Archaea.Methanogenic microbes are distributed worldwide inhabiting anaerobic environments not only across a broad range of diverse ecosystem but also inhabiting similar ecosystem located across a broad range of environmental and climatic conditions in different latitudes. The genus Methanobacterium holds the greater cultured species diversity (21 species until 2013). Members in this group have been isolated from various sources including marine to terrestrial environments. All species are capable of growth by reduction of CO2 with H2, however they present a broad range and variation in phenotypic and genomic characteristics including catabolism of substrates or G+C content (30-57%). We investigate the source and long-term consequences of the observed diversity within the Methanobacterium genus as a model group capable of wide distribution across northern and southern wetlands.