Variants of the Obligate Methanotroph Isolate 761M Capable of Growth on Glucose in the Absence of Methane

Effects of changes in throughfall on soil GHG fluxes under a mature temperate forest, northeastern China

Climate change scenarios predict a change in the rainfall regimes for this current century, which has different impacts on soil greenhouse gas (GHG) fluxes. However, how changes in annual rainfall affect annual GHG fluxes of forest soils remain unknown. A six-year field experiment with -25% and -50% throughfall (TF) and +25% TF manipulation was performed to explore the mechanisms involving GHG fluxes under a mature temperate forest, northeastern China and to work out whether the TF effect sizes on annual soil GHG fluxes vary with dry and wet years. The results showed that both -25% TF and -50% TF treatments depressed annual soil nitrous oxide (N₂O) and carbon dioxide (CO₂) emissions but increased annual soil methane (CH₄) uptake. A contrary pattern of annual soil GHG fluxes was observed in the +25% TF treatment. When annual TF input was decreased by 100 mm, annual soil N₂O and CO₂ emissions were decreased by 18.1 ± 3.1 mg N m^-2 and by 39.4 ± 6.1 g C m^-2 during the growing season, respectively, and annual soil CH₄ uptake was increased by 11.5 ± 3.4 mg C m^-2. Both -25% TF and -50% TF treatments reduced annual soil dissolved organic C (DOC) leaching by 29.3% and 45.6% and dissolved total N (DN) leaching by 30.8% and 39.6%, respectively. Contrary to annual soil N₂O and CO₂ emissions, annual soil CH₄ uptake during the growing season significantly decreased with an increase in the annual leaching fluxes of soil DOC, inorganic N, and DN. Besides soil moisture and temperature and pH, soil GHG fluxes under manipulating TF condition were regulated by soil labile C and N status. Our findings indicated that the TF effect sizes on both annual GHG fluxes and net annual GHG balance (GWP) of forest soils varied with dry and wet years in northeastern China. The results highlight the importance of altered annual rainfall in regulating annual soil GHG fluxes and the GWP in temperate forests under global climate change.

Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis

The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners. Our study revealed that key metabolic functions are most likely accomplished jointly by B. azoricus and its symbionts: (1) CO₂ is pre-concentrated by the host for carbon fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing symbiont. In return (3), the sulfur oxidizer may compensate for the host's putative deficiency in amino acid and cofactor biosynthesis. We also identified numerous ‘symbiosis-specific' host proteins by comparing symbiont-containing and symbiont-free host tissues and symbiont fractions. These proteins included a large complement of host digestive enzymes in the gill that are likely involved in symbiont digestion and carbon transfer from the symbionts to the host.

Synergistic effects of dissolved organic carbon and inorganic nitrogen on methane uptake in forest soils without and with freezing treatment

There is limited knowledge about how the interaction of dissolved organic carbon (DOC) and inorganic nitrogen (N) released into the soil just after freezing can affect methane (CH₄) uptake in forest soils. Here, we present how freezing treatment and glucose, as a DOC source, can affect the roles of NH₄⁺-N and NO₃⁻-N in inhibiting soil CH₄ uptake, by using soil-core incubation experiments. A long-term freezing at low temperature reduced cumulative CH₄ uptake in the soils sampled from two temperate forest stands without carbon (C) and N addition. The inhibition effects of N addition as NH₄Cl and KNO₃ on the soil CH₄ uptake were much larger than C addition. Freezing treatment eliminated the inhibition effect of NH₄Cl and KNO₃ addition on CH₄ uptake, and this response was affected by glucose addition and forest types. The addition of glucose eliminated the inhibition effect of NO₃⁻-N on CH₄ uptake in the forest soils without and with freezing treatment, while the addition of NH₄⁺-N and glucose inhibited synergistically the soil CH₄ uptake. The results highlight the importance of synergistic effects of DOC and N inputs on the soil CH₄ uptake under forest stands during soil wetting and thawing periods.

Methanol promotes atmospheric methane oxidation by methanotrophic cultures and soils

Two methanotrophic bacteria, Methylobacter albus BG8 and Methylosinus trichosporium OB3b, oxidized atmospheric methane during batch growth on methanol. Methane consumption was rapidly and substantially diminished (95% over 9 days) when washed cell suspensions were incubated without methanol in the presence of atmospheric methane (1.7 ppm). Methanotrophic activity was stimulated after methanol (10 mM) but not methane (1,000 ppm) addition. M. albus BG8 grown in continuous culture for 80 days with methanol retained the ability to oxidize atmospheric methane and oxidized methane in a chemostat air supply. Methane oxidation during growth on methanol was not affected by methane deprivation. Differences in the kinetics of methane uptake (apparent K(m) and V(max)) were observed between batch- and chemostat-grown cultures. The V(max) and apparent K(m) values (means +/- standard errors) for methanol-limited chemostat cultures were 133 +/- 46 nmol of methane 10 cells h and 916 +/- 235 ppm of methane (1.2 muM), respectively. These values were significantly lower than those determined with batch-grown cultures (V(max) of 648 +/- 195 nmol of methane 10 cells h and apparent K(m) of 5,025 +/- 1,234 ppm of methane [6.3 muM]). Methane consumption by soils was stimulated by the addition of methanol. These results suggest that methanol or other nonmethane substrates may promote atmospheric methane oxidation in situ.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.

Effects of hydrocarbon enrichment on trichloroethylene biodegradation and microbial populations in finished compost

This study focused on the capacity of finished compost, often used as packing material in biofiltration units, to support microbial biodegradation of trichloroethylene (TCE). Finished compost was enriched with methane or propane (10% head space) to stimulate cometabolic biodegradation of gaseous TCE. Successful hydrocarbon enrichment, as indicated by rapid depletion of hydrocarbon gas and measurable growth of hydrocarbon-utilizing micro-organisms, occurred within a week. Within batch reactor flasks, approximately 75% of head space TCE (1-40 ppmv) was rapidly sorbed onto compost material. Up to 99% of the remaining head space TCE was removed via biodegradation in compost enriched with either hydrocarbon. Hydrocarbon enrichment with methane or propane corresponded to 10-fold increases in methanotrophic or propanotrophic populations, respectively. Based on growth assessment under different nutritional regimes, there appeared to be complex metabolic interactions within the microbial community in enriched compost. Five separate bacterial cultures were derived from the hydrocarbon-enriched compost and assayed for the ability to degrade TCE.

Methanotrophic bacteria

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene.

Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria

Fifteen small-subunit rRNAs from methylotrophic bacteria have been sequenced. Comparisons of these sequences with 22 previously published sequences further defined the phylogenetic relationships among these bacteria and illustrated the agreement between phylogeny and physiological characteristics of the bacteria. Phylogenetic trees were constructed with 16S rRNA sequences from methylotrophic bacteria and representative organisms from subdivisions within the class Proteobacteria on the basis of sequence similarities by using a weighted least-mean-square difference method. The methylotrophs have been separated into coherent clusters in which bacteria shared physiological characteristics. The clusters distinguished bacteria which used either the ribulose monophosphate or serine pathway for carbon assimilation. In addition, methanotrophs and methylotrophs which do not utilize methane were found to form distinct clusters within these groups. Five new deoxyoligonucleotide probes were designed, synthesized, labelled with digoxigenin-11-ddUTP, and tested for the ability to hybridize to RNA extracted from the bacteria represented in the unique clusters and for the ability to detect RNAs purified from soils enriched for methanotrophs by exposure to a methane-air atmosphere for one month. The 16S rRNA purified from soil hybridized to the probe which was complementary to sequences present in 16S rRNA from serine pathway methanotrophs and hybridized to a lesser extent with a probe complementary to sequences in 16S rRNAs of ribulose monophosphate pathway methanotrophs. The nonradioactive detection system used performed reliably at amounts of RNA from pure cultures as small as 10 ng.

Biodegradation of chlorinated ethenes by a methane-utilizing mixed culture

Chlorinated ethenes are toxic substances which are widely distributed groundwater contaminants and are persistent in the subsurface environment. Reports on the biodegradation of these compounds under anaerobic conditions which might occur naturally in groundwater show that these substances degrade very slowly, if at all. Previous attempts to degrade chlorinated ethenes aerobically have produced conflicting results. A mixed culture containing methane-utilizing bacteria was obtained by methane enrichment of a sediment sample. Biodegradation experiments carried out in sealed culture bottles with radioactively labeled trichloroethylene (TCE) showed that approximately half of the radioactive carbon had been converted to 14CO2 and bacterial biomass. In addition to TCE, vinyl chloride and vinylidene chloride could be degraded to products which are not volatile chlorinated substances and are therefore likely to be further degraded to CO2. Two other chlorinated ethenes, cis and trans-1,2-dichloroethylene, were shown to degrade to chlorinated products, which appeared to degrade further. A sixth chlorinated ethene, tetrachloroethylene, was not degraded by the methane-utilizing culture under these conditions. The biodegradation of TCE was inhibited by acetylene, a specific inhibitor of methane oxidation by methanotrophs. This observation supported the hypothesis that a methanotroph is responsible for the observed biodegradations.