Formyltetrahydrofolate Synthetase Sequences from Salt Marsh Plant Roots Reveal a Diversity of Acetogenic Bacteria and Other Bacterial Functional Groups

Abstract

Sixty-two partial formyltetrahydrofolate synthetase (FTHFS) structural gene sequences were recovered from roots of salt marsh plants, including Spartina alterniflora, Salicornia virginica, and Juncus roemerianus. Only S. alterniflora roots yielded sequences grouping with FTHFS sequences from known acetogens. Most other FTHFS or FTHFS-like sequences grouped with those from sulfate-reducing bacteria. Several sequences that grouped with Sphingomonas paucimobilis ligH were also recovered.The acetogens are anaerobic bacteria that utilize the acetylcoenzyme A (CoA) pathway for synthesis of acetyl-CoA from C 1 compounds (6, 33). The acetogens are diverse (6, 29, 31), physiologically versatile (3, 7, 33), and apparently ubiquitous in anoxic and suboxic environments (7). It is not unlikely that acetogens are ecologically significant producers of acetate, a key intermediate in terminal carbon metabolism, in many environments.Salt marshes are among the most productive ecosystems known. Much of salt marsh terminal carbon metabolism occurs in saturated, anoxic sediments and is due to sulfate-reducing bacteria or, in deeper, sulfate-limited sediments, to methanogenic Archaea. The root zones of salt marsh plants are foci of high microbial biomass and intensive activity by bacteria (reviewed in reference 20). These bacteria occur in sediments impacted by the roots (the rhizosphere), on the root surfaces (the rhizoplane), and within the root cortex (the endorhizosphere) (5,20). Despite intermittent oxygen availability in the rhizospheres of salt marsh plants due to gas transport processes (13, 32), root-associated anaerobes, including sulfate reducers, methanogens, and acetogens, have been previously documented (9,12,(19)(20)(21)27). Recently, Küsel et al. (17) demonstrated the presence of acetogenic bacteria in the rhizoplane and endorhizosphere of the seagrass Halodule wrightii. With the exception of recovery of a few partial sequences of the structural gene encoding the acetyl-CoA pathway enzyme, formyltetrahydrofolate synthetase (FTHFS), from roots of the dominant cordgrass Spartina alterniflora (19), there has been no investigation of salt-marsh-plant-associated acetogens or acetogenesis. Consequently, we have little knowledge of what types of plants might harbor these organisms or what types of acetogens might be associated with salt marsh plants.In this study, we have recovered and phylogenetically analyzed partial FTHFS sequences to examine the diversity of acetogenic and other FTHFS-containing bacteria associated with roots of dominant salt marsh plants. We found a clear demarcation between sequences recovered from the low-marsh dominant S. alterniflora (smooth cordgrass; designated Spartina hereafter) and those from two common high-marsh plants, Salicornia virginica (common pickleweed; designated Salicornia hereafter) and Juncus roemerianus (black needlerush; designated Juncus hereafter).Live roots were collected from Salicornia, Juncus, and the short and tall growth forms of Spartina from the Crab Haul Creek basin ...

Syntrophic Acetate-Oxidizing Microbes in Methanogenic Environments

“…Also, applications of a functional gene for formyl-THF synthetase implied the presence of phylogenetically diverse acetogens in several natural habitats 34,35,46,48,49,54) . Considering that many previously isolated syntrophic acetate-oxidizing bacteria are acetogens, these acetate syntrophs may potentially be distributed more widely in various environments than previously thought.…”

Carbon Isotope Fractionation of 11 Acetogenic Strains Grown on H 2 and CO 2

“…Thus, the fractionation factor for total acetate (ε acetate total ϭ Ϫ57.3‰ Ϯ 2.3‰) was similar to that of the methyl group of acetate (ε methyl ϭ Ϫ58.2‰ Ϯ 3.1‰). These data have frequently been used to interpret environmental isotopic signatures of acetate in, for example, lake sediments (14-19), rice paddies (20-23), and marine environments (24-27).However, this reported value may not cover all acetogens, since they are metabolically, ecologically, and phylogenetically diverse (25,(28)(29)(30). We know from different methanogenic archaea, which likewise utilize the acetyl-CoA pathway to produce CH 4 from H 2 and CO 2 , that the fractionation factors range from Ϫ25‰ (31) to Ϫ69‰ (32; reviewed in reference 9).…”

“…However, this reported value may not cover all acetogens, since they are metabolically, ecologically, and phylogenetically diverse (25,(28)(29)(30). We know from different methanogenic archaea, which likewise utilize the acetyl-CoA pathway to produce CH 4 from H 2 and CO 2 , that the fractionation factors range from Ϫ25‰ (31) to Ϫ69‰ (32; reviewed in reference 9).…”

Changes in the Acetogenic Population in a Mesophilic Anaerobic Digester in Response to Increasing Ammonia Concentration

“…Degenerated primers, designed to target a functional gene encoding a key enzyme in this pathway, 10-formyltetrahydrofolate synthetase (FTHFS) (11), have been used in several investigations to study acetogenic populations in different environments, such as salt marshes (12), hindguts (19), anaerobic sludge (21), human faeces (17) and microbial electrolysis cells (18).…”