Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil

A Cr(VI)-resistant, Gram-positive, spore-forming, obligate anaerobe, designated GCAF-1T, was isolated from chromium-contaminated soil by its ability to reduce Cr(VI) in low concentrations. Mixed acid fermentation during growth on glucose resulted in accumulation of acetate, butyrate, formate and lactate. Morphological studies indicated the presence of peritrichous flagella, pili and an S-layer. The major cellular fatty acids (>5 %) were C16 : 0, C14 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), C18 : 1ω7c, C16 : 1ω9c, summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B) and C18 : 1ω9c. The DNA G+C content of strain GCAF-1T was 30.7 mol%. Phylogenetic interference indicated that strain GCAF-1T clustered with group I of the genus Clostridium. Of strains within this cluster, strain GCAF-1T shared the highest 16S rRNA gene sequence similarities (98.1–98.9 %) with Clostridium beijerinckii DSM 791T, C. saccharobutylicum NCP 262T, C. saccharoperbutylacetonicum N1-4T, C. puniceum DSM 2619T and C. roseum DSM 51T. However, strain GCAF-1T could be clearly distinguished from its closest phylogenetic neighbours by low levels of DNA–DNA relatedness (<50 %) and some phenotypic features. Based on the evidence presented here, strain GCAF-1T ( = DSM 23318T  = KCTC 5935T) represents a novel species of the genus Clostridium, for which the name Clostridium chromiireducens sp. nov. is proposed.

Effects of DNA polymer length on its adsorption to soils

Three different DNA fragments ranging size from 2.69 kbp (1.75 MDa) to 23 kbp (14.95 MDa) were used as tracers to study the adsorption of polydisperse solutions of calf thymus DNA to eight model soils. The adsorption of the three tracers to all soils was described by the Freundlich adsorption model, with adsorption coefficients (K) ranging from 1.1 for acid-washed sand to over 300 for one soil. An inverse relationship between tracer size and K was observed with six of the eight soils, indicating that smaller fragments are sorbed preferentially versus larger fragments in these soils. No significant correlation between K and the organic carbon contents, clay contents, pHs, or cation exchange capacities of the model soils was observed.

Syntrophic-archaeal associations in a nutrient-impacted freshwater marsh

AIMS

Evaluation of the composition, distribution and activities of syntrophic bacteria and methanogens in soils from eutrophic and low nutrient regions of a freshwater marsh, and to compare these results with those obtained from a similar study in the Florida Everglades.

METHODS AND RESULTS

Culture dependent and independent approaches were employed to study consortia of syntrophs and methanogens in a freshwater marsh. Methanogenesis from butyrate oxidation was fourfold higher in microcosms containing soil from eutrophic regions of the marsh than from low nutrient regions. Propionate was oxidized in eutrophic microcosms at lower rates than butyrate and with lower yields of methane. Sequence analysis of 16S rRNA gene clone libraries from DNA extracted from microcosms and soils revealed differences such that the dominant restriction fragment length polymorphism (RFLP) phylotypes (representing 82-88% of clone libraries) from eutrophic soils clustered with fatty acid oxidizing Syntrophomonas spp. The four dominant RFLP phylotypes (representing 11-24%) from microcosms containing soils from low nutrient regions were sequenced, and clustered with micro-organisms having the potential for fermentative and syntrophic metabolism. Archaeal 16S rRNA sequence analysis showed that methanogens from eutrophic regions were from diverse families, including Methanomicrobiaceae, Methanosarcinaceae, and Methanocorpusculaceae, but clone libraries from low nutrient soils revealed only members of Methanosarcinaceae.

CONCLUSIONS

These findings indicate that syntroph-methanogen consortia differed with nutrient levels in a freshwater marsh.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is one of few studies addressing the distribution of fatty acid consuming-hydrogen producing bacteria (syntrophs) and their methanogenic partners in wetland soils, and the effects of eutrophication on the ecology these groups.

Characterization of methanogenic and methanotrophic assemblages in landfill samples

A greater understanding of the tightly linked trophic groups of anaerobic and aerobic bacteria residing in municipal solid waste landfills will increase our ability to control methane emissions and pollutant fate in these environments. To this end, we characterized the composition of methanogenic and methanotrophic bacteria in samples taken from two regions of a municipal solid waste landfill that varied in age. A method combining polymerase chain reaction amplification, restriction fragment length polymorphism analysis and phylogenetic analysis was used for this purpose. 16S rDNA sequence analysis revealed a rich assemblage of methanogens in both samples, including acetoclasts, H2/CO2-users and formate-users in the newer samples and H2/CO2-users and formate-users in the older samples, with closely related genera including Methanoculleus, Methanofollis, Methanosaeta and Methanosarcina. Fewer phylotypes of type 1 methanotrophs were observed relative to type 2 methanotrophs. Most type 1 sequences clustered within a clade related to Methylobacter, whereas type 2 sequences were broadly distributed among clades associated with Methylocystis and Methylosinus species. This genetic characterization tool promises rapid screening of landfill samples for genotypes and, therefore, degradation potentials.

Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils

Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G + C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100-10,000 Pasteuria endospores (g soil)(-1).

Degradation of 1,3-dichloropropene by a soil bacterial consortium and Rhodococcus sp. AS2C isolated from the consortium

A bacterial consortium capable of degrading the fumigant 1,3-D ((Z)- and (E)- 1,3-dichloropropene) was enriched from an enhanced soil. This mixed culture degraded (Z)- and (E)-1,3-D only in the presence of a suitable biodegradable organic substrate, such as tryptone, tryptophan, or alanine. After 8 months of subculturing at 2- to 3-week intervals, a strain of Rhodococcus sp. (AS2C) that was capable of degrading 1,3-D cometabolically in the presence of a suitable second substrate was isolated. (Z)-3-chloroallyl alcohol (3-CAA) and (Z)-3-chloroacrylic acid (3-CAAC), and (E)-3-CAA and (E)-3-CAAC were the metabolites of (Z)- and (E)- 1,3-D, respectively. (E)- 1,3-D was degraded faster than (Z)- 1,3-D by the strain AS2C and the consortium. AS2C also degraded (E)-3-CAA faster than (Z)-3-CAA. Isomerization of (E)- 1,3-D to (Z)- 1,3-D or the (Z) form to the (E) form did not occur.

Carbofuran degradation in soil profiles

Two soils, Puyallup fine sandy loam from Puyallup, WA, and Ellzey fine sand from Hastings, FL, each with a prior history of carbofuran exposure but with different pedological and climatological characteristics, were found to exhibit enhanced degradation toward carbofuran in surface and subsurface soil layers. The treated Puyallup and Ellzey soils exhibited higher mineralization rates for both the carbonyl and the aromatic ring of carbofuran when compared to untreated soils. Disappearance rates of [14C-URL (uniformly ring labeled)] carbofuran in the treated Ellzey soil was faster than in untreated soil, and also faster in surface soil than in subsurface soil. Initial degradation patterns in the treated Ellzey soil were also different from those in the untreated soil. The treated Ellzey soil degraded carbofuran mainly through biological hydrolysis, while untreated soil degraded carbofuran through both oxidative and hydrolytic processes.

Effects of sorption on biological degradation rates of (2,4-dichlorophenoxy) acetic acid in soils

Three mathematical models were proposed to describe the effects of sorption of both bacteria and the herbicide (2,4-dichlorophenoxy)acetic acid (2,4-D) on the biological degradation rates of 2,4-D in soils. Model 1 assumed that sorbed 2,4-D is not degraded, that only bacteria in solution are capable of degrading 2,4-D in solution, and that sorbed bacteria are not capable of degrading either sorbed or solution 2,4-D. Model 2 stated that only bacteria in the solution phase degrade 2,4-D in solution and that only sorbed bacteria degrade sorbed 2,4-D. Model 3 proposed that sorbed 2,4-D is completely protected from degradation and that both sorbed and solution bacteria are capable of degrading 2,4-D in solution. These models were tested by a series of controlled laboratory experiments. Models 1 and 2 did not describe the data satisfactorily and were rejected. Model 3 described the experimental results quite well, indicating that sorbed 2,4-D was completely protected from biological degradation and that sorbed- and solution-phase bacteria degraded solution-phase 2,4-D with almost equal efficiencies.