Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria.

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.

Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov.

One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.

Specificities and commonalities of the Planctomycetes plasmidome.

Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.

Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes.

Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.

Stratiformator vulcanicus gen. nov., sp. nov., a marine member of the family Planctomycetaceae isolated from a red biofilm in the Tyrrhenian Sea close to the volcanic island Panarea.

A novel planctomycetal strain, designated Pan189T, was isolated from biofilm material sampled close to Panarea Island in the Tyrrhenian Sea. Cells of strain Pan189T are round grain rice-shaped, form pink colonies and display typical planctomycetal characteristics including asymmetric cell division through polar budding and presence of crateriform structures. Cells bear a stalk opposite to the division pole and fimbriae cover the cell surface. Strain Pan189T has a mesophilic (optimum at 24 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. Under laboratory-scale cultivation conditions, it reached a generation time of 102 h (µmax = 0.0068 h-1), which places the strain among the slowest growing members of the phylum Planctomycetota characterized so far. The genome size of the strain is with 5.23 Mb at the lower limit among the family Planctomycetaceae (5.1-8.9 Mb). Phylogenetically, the strain represents a novel genus and species in the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. We propose the name Stratiformator vulcanicus gen. nov., sp. nov. for the novel taxon, that is represented by the type strain Pan189T (= DSM 101711 T = CECT 30699 T).

Does a Diet Rich in the Bacterium Rhodopirellula rubra Improve Daphnia magna Performance?

BACKGROUND: In the wild various organisms contribute to daphnids diet. This study, intendeds to evaluate the potential of the concentration of Rhodopirellula rubra as a single or supplementary food source for Daphnia magna. METHODS: Feeding assays were performed according to standard guidelines for chronic assays (21 days), and life-history parameters and several biomarkers (protein content, oxidative stress, energetic reserves and pigments) were measured. Five food regimens were conducted with 20 individual replicates (A - R. subcapitata; 0.2 - suspension of R. rubra at 0.2 arbitrary units (AU); 0.4 - suspension of R. rubra at 0.4 AU; 0.2+A - suspension of R. rubra at 0.2+alga; 0.2+A-suspension of R. rubra at 0.4 AU + alga). Additionally, the effects of three diets (A, 0.2, and 0.2+A) on the longevity of D. magna were assessed. RESULTS: The five diets showed a different C, N, and carotenoids composition, with an increase in the mixed diets. The results confirmed that the mixed diets improved D. magna life-history parameters. A decrease in glycogen, and the increase of haemoglobin, protein, and gluthione-S-transferase (GST) were observed. Furthermore, D. magna fed with bacterial single diets, presented worsen life history parameters and a decrease in the protein content. An induction of oxidative stress response (increased catalase and GST), and a significant decrease in lipid peroxidation and an accumulation of glycogen and carotenoids were observed. Overall, an increase in the amount of R. rubra provided to D. magna, from 0.2 AU to 0.4 AU, negatively impacted daphnid performance. No significant effects on Daphnia longevity (a 110-day assay) were observed among the three diets tested. However, a significant survival percentage and fertility (cumulative offspring is more than twice) was observed when D. magna was fed with the mixed diet. CONCLUSIONS: Results demonstrated that different diets provided a nutritional diversified food to the daphnids that induced differences in D. magna performance. The mixed diets proved to be beneficial (with increase in offspring) on D. magna performance, independently of the bacterial concentration tested. When in single diet, bacterial concentration is not nutritionally sufficient to raise D. magna even when in increased concentration.

Anatilimnocola floriformis sp. nov., a novel member of the family Pirellulaceae from a boreal lake, and emended description of the genus Anatilimnocola.

Planctomycetes of the family Pirellulaceae are commonly addressed as budding aquatic bacteria with a complex lifestyle. Although this family is well represented by cultured and taxonomically characterized isolates, nearly all of them were obtained from brackish or marine habitats. The examples of described freshwater Pirellulaceae planctomycetes are limited to two species only, Pirellula staley and 'Anatilimnocola aggregata'. In this study, we characterized a novel freshwater planctomycete of the genus 'Anatilimnocola', strain PX40T, which was isolated from a boreal eutrophic lake. Strain PX40T was represented by budding, unpigmented, ellipsoidal to pear-shaped cells, which often occurred in characteristic flower-like rosettes. Cells were covered by bundles of fimbriae; crateriform-like structures were localized on a reproductive cell pole only. These planctomycetes were obligately aerobic, heterotrophic bacteria that utilized various sugars and some polysaccharides, and were highly sensitive to NaCl. Growth occurred in the pH range 5.0-7.5 (with an optimum at pH 6.5-7.0), and at temperatures between 15 and 30 °C (with an optimum at 22-25 °C). The major fatty acids of strain PX40T were C18:1ω9c, C16:0, and 16:1ω7c; cells also contained a wide variety of hydroxy- and dihydroxy-fatty acids and a C31:9 alkene. The major intact polar lipids were diacylglyceryl-(N,N,N)-trimethylhomoserines. The 16S rRNA gene sequence of strain PX40T displayed 96.6% similarity to that of 'Anatilimnocola aggregata' ETA_A8T. The genome of strain PX40T was 8.93 Mb in size and contained one copy of rRNA operon, 76 tRNA genes and 7092 potential protein-coding genes. The DNA G+C content was 57.8%. The ANI value between strain PX40T and 'Anatilimnocola aggregata' ETA_A8T was 78.3%, suggesting that these planctomycetes represent distinct species. We, therefore, propose a novel species of the genus 'Anatilimnocola', 'A. floriformis' sp. nov., with strain PX40T (= KCTC 92369T = VKM B-3621T = UQM 41463T) as the type strain.

Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate.

Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.

Isolation, diversity and antimicrobial activity of planctomycetes from the Tejo river estuary (Portugal).

The discovery of new bioactive compounds is an invaluable aid to the development of new drugs. Strategies for finding novel molecules can focus on the exploitation of less studied organisms and ecosystems such as planctomycetes and brackish habitats. The unique cell biology of the underexplored Planctomycetota mean it is of particular interest. In this study, we aimed to isolate planctomycetes from the estuary of the Tejo river (Portugal). To reach this goal, macroalgae, water and sediments were sampled and diverse media and isolation techniques applied. Sixty-nine planctomycetal strains were brought into pure culture. An analysis of the 16S rRNA genes found that the majority of the isolates were affiliated to the genus Rhodopirellula. Putative novel taxa belonging to genera Stieleria and Rhodopirellula were also isolated and characterized morphologically. Enterobacterial repetitive intergenic consensus fingerprinting analyses showed higher diversity and different genotypes within close strains. Relevant biosynthetic gene clusters were found in most isolates and acetone extracts from representative strains exhibited mild antimicrobial activities against Escherichia coli and Staphylococcus aureus. Our work has not only enlarged the number and diversity of cultured planctomycetes but has also shown the potential for the discovery of bioactive compounds from the novel taxa.

A genomic overview including polyphasic taxonomy of Thalassoroseus pseudoceratinae gen. nov., sp. nov. isolated from a marine sponge, Pseudoceratina sp.

A pink-coloured, salt- and alkali-tolerant planctomycetal strain (JC658T) with oval to pear-shaped, motile, aerobic, Gram-negative stained cells was isolated from a marine sponge, Pseudoceratina sp. Strain JC658T shares the highest 16S rRNA gene sequence identity with Maioricimonas rarisocia Mal4T (< 89.2%) in the family Planctomycetaceae. The genomic analysis of the new strain indicates its biotechnological potential for the production of various industrially important enzymes, notably sulfatases and carbohydrate-active enzymes (CAZymes), and also potential antimicrobial compounds. Several genes encoding restriction-modification (RM) and CRISPR-CAS systems are also present. NaCl is obligate for growth, of which strain JC658T can tolerate a concentration up to 6% (w/v). Optimum pH and temperature for growth are 8.0 (range 7.0-9.0) and 25 ºC (range 10-40 °C), respectively. The major respiratory quinone of strain JC658T is MK6. Major fatty acids are C16:1ω7c/C16:1ω6c, C18:0 and C16:0. Major polar lipids are phosphatidylcholine, phosphatidyl-dimethylethanolamine and phosphatidyl-monomethylethanolamine. The genomic size of strain JC658T is 7.36 Mb with a DNA G + C content of 54.6 mol%. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strain JC658T belongs to a novel genus and constitutes a novel species within the family Planctomycetaceae, for which we propose the name Thalassoroseus pseudoceratinae gen. nov., sp. nov. The novel species is represented by the type strain JC658T (= KCTC 72881 T = NBRC 114371 T).

Complete genome sequence of the cellulolytic planctomycete Telmatocola sphagniphila SP2T and characterization of the first cellulolytic enzyme from planctomycetes.

Planctomycetes of the family Gemmataceae are strictly aerobic chemo-organotrophs that display a number of hydrolytic capabilities. A member of this family, Telmatocola sphagniphila SP2T, is the first described planctomycete with experimentally proven ability for growth on cellulose. In this study, the complete genome sequence of strain SP2T was obtained and the genome-encoded determinants of its cellulolytic potential were analyzed. The T. sphagniphila SP2T genome was 6.59 Mb in size and contained over 5200 potential protein-coding genes. The search for enzymes that could be potentially involved in cellulose degradation identified a putative cellulase that contained a domain from the GH44 family of glycoside hydrolases. Homologous enzymes were also revealed in the genomes of two other Gemmataceae planctomycetes, Zavarzinella formosa A10T and Tuwongella immobilis MBLW1T. The gene encoding this predicted cellulase in strain SP2T was expressed in E. coli and the hydrolytic activity of the recombinant enzyme was confirmed in tests with carboxymethyl cellulose but not with crystalline cellulose, xylan, mannan or laminarin. This is the first experimentally characterized cellulolytic enzyme from planctomycetes.

Development of a chemically defined medium for Planctopirus limnophila to increase biomass production

BACKGROUND Planctomycetes is a phylum of biofilm-forming bacteria with numerous biosynthetic gene clusters, offering a promising source of new bioactive secondary metabolites. However, the current generation of chemically defined media achieves only low biomass yields, hindering research on these species. We therefore developed a chemically defined medium for the model organism Planctopirus limnophila to increase biomass production. RESULTS We found that P. limnophila grows best with a 10 mM sodium phosphate buffer. The replacement of complex nitrogen sources with defined amino acid solutions did not inhibit growth. Screening for vitamin requirements revealed that only cyanocobalamin (B12) is needed for growth. We used response surface methodology to optimize the medium, resulting in concentrations of 10 g/L glucose, 34 mL/L Hutner's basal salts, 23.18 mM KNO3, 2.318 mM NH4Cl and 0.02 mg/L cyanocobalamin. The analysis of amino acid consumption allowed us to develop a customized amino acid solution lacking six of the amino acids present in Aminoplasmal 10%. Fed-batch cultivation in a bioreactor using the optimized medium achieved a final DOD600 of 46.8 ± 0.5 after 108 h, corresponding to a cell dry weight of 13.6 ± 0.7 g/L. CONCLUSIONS The optimized chemically defined medium allowed us to produce larger amounts of biomass more quickly than reported in earlier studies. Further research should focus on triggering P. limnophila biofilm formation to activate the gene clusters responsible for secondary metabolism

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community.

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator.

Cysteine Synthase (CS), the enzyme that synthesizes cysteine, performs non-canonical regulatory roles by binding and modulating functions of disparate proteins. Beyond its role in catalysis and regulation in the cysteine biosynthesis pathway, it exerts its moonlighting effect by binding to few other proteins which possess a C-terminal "CS-binding motif", ending with a terminal ILE. Therefore, we hypothesized that CS might regulate many other disparate proteins with the "CS-binding motif". In this study, we developed an iterative sequence matching method for mapping moonlighting biochemistry of CS and validated our prediction by analytical and structural approaches. Using a minimal protein-peptide interaction system, we show that five previously unknown CS-binder proteins that participate in diverse metabolic processes interact with CS in a species-specific manner. Furthermore, results show that signatures of protein-protein interactions, including thermodynamic, competitive-inhibition, and structural features, highly match the known CS-Binder, serine acetyltransferase (SAT). Together, the results presented in this study allow us to map the extreme multifunctional space (EMS) of CS and reveal the biochemistry of moonlighting space, a subset of EMS. We believe that the integrated computational and experimental workflow developed here could be further modified and extended to study protein-specific moonlighting properties of multifunctional proteins.

Phylo-taxogenomics of the genus Tautonia with descriptions of Tautonia marina sp. nov., Tautonia rosea sp. nov., and emended description of the genus.

Four strains of Planctomycetes, (JC636, JC649, JC650T, JC657T) which are all salt and alkali tolerant, pink coloured, with spherical to oval shaped, Gram-stain-negative, non-motile cells were isolated from different regions of Chilika lagoon, India. All strains have obligate requirement for N-acetylglucosamine (NAG) and share highest 16S rRNA gene sequence identity with members of the genus Tautonia (<95%) of the family Isosphaeraceae. The 16S rRNA gene sequence identity between strains was >99.5%. Respiratory quinone for all the strains was MK6. Major fatty acids of all the strains were C18:1ω9c, C16:0 and C18:0. Major polar lipid of the strain JC650T was phosphatidylethanolamine, while, phosphatidylcholine and phosphatidylglycerol for strain JC657T. Spermidine was the only common polyamine for all the four strains. Strains JC657T, JC636 and JC649 shared highest phenotypic similarity along with 100% 16S rRNA gene sequence identity. Strains JC657T, JC636 and JC649 differed from strain JC650T phenotypically, chemotaxonomically and genotypically, thus belong to a different species. The genomic size of strain JC650T and JC657T are 7.06 Mb and 6.96 Mb with DNA G + C content of 63.9 and 62.7 mol%, respectively. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strains JC650T and JC657T (together with strains JC636, JC649) belong to the genus Tautonia and constitute two novel species for which we propose the names Tautonia marina sp. nov., and Tautonia rosea sp. nov., respectively. These two novel species are represented by the type strains JC650T (=KCTC 72177T = NBRC 113885T) and JC657T (=KCTC 72597T = NBRC 113883T) respectively.

Aquisphaera insulae sp. nov., a new member in the family Isosphaeraceae, isolated from the floating island of Loktak lake and emended description of the genus Aquisphaera.

Strain JC669T was isolated from a floating island of Loktak lake, Manipur, India and shares the highest 16S rRNA gene sequence identity with Aquisphaera giovannonii OJF2T. The novel strain is aerobic, Gram negative, light pink-coloured, non-motile, NaCl intolerant and spherical to oval-shaped. It grows in the form of single cells or aggregates and possibly forms structures which appear like fruiting bodies. Strain JC669T grows well up to pH 9.0.The isolate produces MK-6 as respiratory quinone, C18:1ω9c, C16:0 and C18:0 as major fatty acids and phosphatidylcholine, an unidentified amino lipid, an unidentified choline lipid (UCL) and six additional unidentified lipids (UL1, 2, 3, 4, 5, 6) as polar lipids. Strain JC669T has a large genome size of 10.04 Mb and the genomic G + C content was 68.5 mol%. The genome contained all genes essential for lycopene related carotenoid biosynthesis. The polyphasic analysis of its phylogenetic position, morphological, physiological and genomic features supports the classification of strain JC669T as a novel species of the genus Aquisphaera, for which we propose the name Aquisphaera insulae sp. nov. Strain JC669T (= KCTC 72672T = NBRC 114306T) is the type strain of the novel species.

Heterologous Expression of Thermogutta terrifontis Endo-Xanthanase in Penicillium verruculosum, Isolation and Primary Characterization of the Enzyme.

Heterologous endo-xanthanase (EX) from the thermophilic planktomycete Thermogutta terrifontis strain was obtained using Penicillium verruculosum 537 (ΔniaD) expression system with the cellobiohydrolase 1 gene promoter. Homogeneous EX with a molecular weight of 23.7 kDa (pI 6.5) was isolated using liquid chromatography methods. This xanthan degrading enzyme also possesses the enzymatic activity towards CM-cellulose, ß-glucan, curdlan, lichenan, laminarin, galactomannan, xyloglucan but not towards p-nitrophenyl derivatives of ß-D-glucose, mannose and cellobiose. The temperature and pH optima of EX were 55°C and 4.0, respectively; the enzyme exhibited 90% of its maximum activity in the temperature range 50-60°C and pH 3-5.

Genomic analysis reveals the potential for hydrocarbon degradation of Rhodopirellula sp. MGV isolated from a polluted Brazilian mangrove.

Planctomycetes are bacteria found in several environments, such as mangroves. In the coastline of the State of Sao Paulo (Brazilian Southeast), mangroves occur in different stages of environmental contamination, promoted by the proximity to the city and industrial activities. One of these mangroves (located in the city of Bertioga) is characterized by the high impact due to past petroleum and ongoing urban contamination. We isolated five bacteria affiliated to Planctomycetes from this mangrove and further subjected them to phenotypical and genetic analysis. The tolerance for salinity was demonstrated by the cultivation under distinct concentrations of NaCl. The ability of this bacterium to use diverse carbon sources was revealed by the use of 30 C-sources from a total of 31 tests. We found the isolate Rhodopirellula sp. MGV very closely affiliated to species of the genus Rhodopirellula, harboring a genome with 7.16 Mbp and 55.3% of GC. The annotation of the 77 contigs resulted in 6.284 CDS, with a remarkable occurrence of sequences associated with aromatic carbon metabolism. In conclusion, we present the isolation and characterization of a Planctomycetes from mangroves, suggesting its participation in the degradation of hydrocarbons present in the contaminated mangroves studied.

Comparison of neutral lipid fatty acid composition in organisms from different trophic levels.

The profiles of total fatty acids (TFAs) and the neutral lipid fatty acids (NLFAs) were compared for the bacterium Rhodopirellula rubra and the alga Raphidocelis subcapitata (conventional food source for Daphnia magna). D. magna NLFAs were assessed when this crustacean was fed with bacterium and alga, individually or in combination. After NLFA extraction, the profiles of the various organisms were characterized by gas chromatography. Results evidenced the relevance of the different composition of the fatty acid (FAs) fractions in the different organisms, R. rubra and R. subcapitata. In these species, the NFLA analyses revealed high amounts of long chain FAs (C19). The FA profile of D. magna was influenced by the different diets provided although the preferred diet was the alga. D. magna showed the capacity to adapt to the available food resources as it defines its FA profile according to its needs, namely for the long chain FAs (C19).

Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link.

The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.