Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in <i>Sphagnum</i>-Dominated Northern Wetlands

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses.Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine(TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomyceteisolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) andmolecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) inorder to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout theprofiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundanceof planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliatedwith the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group.Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoyepeat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mossepeat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundantTMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest thatplanctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and thechange in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redoxconditions at the oxic/anoxic interface

<i>Paludisphaera borealis</i> gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of <i>Isosphaeraceae</i> fam. nov.

Two isolates of aerobic, budding, pink-pigmented bacteria, designated strains PX4T and PT1, were isolated from a boreal Sphagnum peat bog and a forested tundra wetland. Cells of these strains were non-motile spheres that occurred singly or in short chains. Novel isolates were capable of growth at pH values between 3.5 and 6.5 (optimum at pH?5.0–5.5) and at temperatures between 6 and 30?°C (optimum at 15–25?°C). Most sugars and a number of polysaccharides including pectin, xylan, lichenin and Phytagel were used as growth substrates. The major fatty acids were C16?:?0, C18?:?1?9 and C18?:?0; the major polar lipids were phosphocholine and trimethylornithine. The quinone was menaquinone-6, and the G+C content of the DNA was 66?mol%. Strains PX4T and PT1 were members of the order Planctomycetales and displayed 93–94?% 16S rRNA gene sequence similarity to Aquisphaera giovannonii, 91–92?% to species of the genus Singulisphaera and 90–91?% to Isosphaera pallida. The two novel strains, however, differed from members of these genera by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Paludisphaera borealis gen. nov., sp. nov., is proposed. The type strain is PX4T (?=?DSM 28747T?=?VKM B-2904T). We also suggest the establishment of a novel family, Isosphaeraceae fam. nov., to accommodate stalk-free planctomycetes with spherical cells, which can be assembled in short chains, long filaments or shapeless aggregates. This family includes the genera Isosphaera, Aquisphaera, Singulisphaera and Paludisphaer

<i>Telmatocola sphagniphila</i> gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (=0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G + C content of the DNA is 58.5–59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. no

Ether- and Ester-Bound iso-Diabolic Acid and Other Lipids in Members of <i>Acidobacteria</i> Subdivision 4

Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting “Candidatus Chloracidobacterium thermophilum”) contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile “Ca. Chloracidobacterium thermophilum.” Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range

Origin and palaeoenvironmental significance of C₂₅ and C₂₇n-alk-1-enes in a 25,000-year lake-sedimentary record from equatorial East Africa

We studied the distribution of long-chain alkenes (n-C23 to n-C31) in well-dated sediments from Lake Challa, a deep crater lake near Mt. Kilimanjaro in equatorial East Africa, to reveal signatures of palaeo-environmental and palaeo-climatic changes affecting the production of these compounds during the last 25 kyr. The apolar fractions of organic sediment extracts dated to the last 16 kyr showed an unusual dominance of d13C-depleted n-C25:1 and n-C27:1 alk-1-enes. These alkenes were not detected in soil and litter from near the shoreline and from the inner rim of the crater, pointing to an autochthonous, aquatic source. Analysis of suspended particulate matter indicated that the n-alk-1-enes are produced in the well-oxygenated upper 30 m of the water column, indicating a phytoplanktonic origin. Sedimenting particles collected monthly from December 2006 to November 2007 showed increased fluxes of n-alk-1-enes following the locally prominent short rain season in November–December. Green algae and/or cyanobacteria were identified as candidate sources of these alkenes. Production of the n-C25:1 and n-C27:1 alkenes in Lake Challa was much reduced during the Last Glacial Maximum and early late-glacial period, suggesting a temperature or CO2 effect on habitat suitability. We explored the potential of n-alk-1-ene accumulation rates, and of a derived Alkene Index [n-C27:1]/([n-C25:1] + [n-C27:1]), to record longer-term climatic changes. The Alkene Index record of Lake Challa over the past 25 kyr shows clear periodicity with a dominant frequency of ~2.3 kyr, potentially indicative of monsoon variability directly or indirectly forced by variation in solar radiation

Acetate degradation at low pH by the moderately acidophilic sulfate reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov.

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2022.816605/full#supplementary-materialIn acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.This work was financed by ERC grants to AS (project 323009) and JS (project 694569), the research program TTW under project number 14797, which is financed by the Dutch Research Council (NWO) to IS-A, and a Gravitation grant (SIAM 024.002.002) of the Netherlands Ministry of Education, Culture and Science to AS and JS.info:eu-repo/semantics/publishedVersio

Identification of novel C25 highly branched isoprenoid thiophene in sediments

A novel C25 highly branched isoprenoid (HBI) thiophene, 2-(2-methylpropyl)-4-[9-(2,6,12-trimethyltetradecyl)]thiophene, has been identified in three sediment samples by isolation followed by characterization by 1H-NMR, GC-MS and Raney Ni desulphurization. This component is probably formed by incorporation of inorganic sulphur species into a specific sedimentary C25 HBI alkadiene. This latter compound is probably derived from diatoms

Free and Bound Fatty-Acids and Hydroxy Fatty-Acids in the Living and Decomposing Eelgrass Zostera-Marina L

Very early diagenetic processes of free, esterified and amide or glycosidically bound fatty acids and hydroxy fatty acids present in well documented samples of living and decomposing eelgrass (Zostera marina L.) were investigated. Free and esterified fatty acids decreased significantly over a period of decay of 12.5 years, although their distribution patterns were largely unchanged. Amide or glycosidically bound alpha-hydroxy fatty acids and the newly recognized alpha,beta-dihydroxy fatty acids were not degraded. Thus both, but in particular the alpha,beta-dihydroxy fatty acids, may serve as potential biomarkers for the recognition of eelgrasses in palaeoenvironments. The increasing amounts of omega-hydroxy fatty acids and alpha,omega-dicarboxylic fatty acids upon decay indicate bacterial transformations of eelgrass lipids. This bacterial action was further demonstrated by a substantial increase of amide-bound beta-hydroxy fatty acids derived from LPS of gram-negative bacteria. [KEYWORDS: Early diagenesis; seagrass; eelgrass; zostera marina l; fatty acids; hydroxy fatty acids; alpha;beta-dihydroxy fatty acids; alpha;omega-dihydroxy fatty acids Sediments; bacteria; lipids; seagrasses; mode; lake]