Identification of a gene essential for sheathed structure formation in Sphaerotilus natans, a filamentous sheathed bacterium

Taxonomic characterization of Sphaerotilus microaerophilus sp. nov., a sheath-forming microaerophilic bacterium of activated sludge origin

A microaerophilic Gram-stain-negative bacilliform bacterial strain, FB-5 T, was isolated from activated sludge in Yokohama, Japan, that exhibited filamentous growth and formed a microtube (sheath). Cells were motile using a single polar flagellum. The optimum growth temperature and pH were 30 °C and 7.5, respectively. Strain FB-5 T was catalase-negative. Peptides and amino acids were utilized as energy and carbon sources. Sugars and organic acids were not utilized. Vitamin B12 enhanced the growth of strain FB-5 T. Sulfur-dependent lithotrophic growth was possible. Major respiratory quinone was UQ-8. Major fatty acids were C16:1ω7 and C16:0. The genomic DNA G + C content was 69.16%. Phylogenetic analysis of the 16S rRNA gene suggested that strain FB-5 T belongs to the genus Sphaerotilus. The close relatives were S. natans subsup. sulfidivorans and S. natans subsup. natans with 98.0% and 97.8% similarity based on the 16S rRNA gene analysis, respectively. The genome size (6.06 Mbp) was larger than that (4.39-5.07 Mbp) of the Sphaerotilus strains. The AAI values against the related strains ranged from 71.0 to 72.5%. The range of ANI values was 81.7 - 82.5%. In addition to these distinguishable features of the genome, the core genome and dDDH analyses suggested that this strain is a novel member of the genus Sphaerotilus. Based on its physiological properties and genomic features, strain FB-5 T is considered as a novel species of the genus Sphaerotilus, for which the name S. microaerophilus sp. nov. is proposed. The type strain is FB-5 T (= JCM 35424 T = KACC 23146 T).

Identification of lthB, a Gene Encoding a Putative Glycosyltransferase Family 8 Protein Required for Leptothrix Sheath Formation

The bacterium Leptothrix cholodnii generates cell chains encased in sheaths that are composed of woven nanofibrils. The nanofibrils are mainly composed of glycoconjugate repeats, and several glycosyltransferases (GTs) are required for its biosynthesis. However, only one GT (LthA) has been identified to date. In this study, we screened spontaneous variants of L. cholodnii SP6 to find those that form smooth colonies, which is one of the characteristics of sheathless variants. Genomic DNA sequencing of an isolated variant revealed an insertion in the locus Lcho_0972, which encodes a putative GT family 8 protein. We thus designated this protein LthB and characterized it using deletion mutants and antibodies. LthB localized adjacent to the cell envelope. ΔlthB cell chains were nanofibril free and thus sheathless, indicating that LthB is involved in nanofibril biosynthesis. Unlike the ΔlthA mutant and the wild-type strain, which often generate planktonic cells, most ΔlthB organisms presented as long cell chains under static conditions, resulting in deficient pellicle formation, which requires motile planktonic cells. These results imply that sheaths are not required for elongation of cell chains. Finally, calcium depletion, which induces cell chain breakage due to sheath loss, abrogated the expression of LthA, but not LthB, suggesting that these GTs cooperatively participate in glycoconjugate biosynthesis under different signaling controls. IMPORTANCE In recent years, the regulation of cell chain elongation of filamentous bacteria via extracellular signals has attracted attention as a potential strategy to prevent clogging of water distribution systems and filamentous bulking of activated sludge in industrial settings. However, a fundamental understanding of the ecology of filamentous bacteria remains elusive. Since sheath formation is associated with cell chain elongation in most of these bacteria, the molecular mechanisms underlying nanofibril sheath formation, including the intracellular signaling cascade in response to extracellular stimuli, must be elucidated. Here, we isolated a sheathless variant of L. cholodnii SP6 and thus identified a novel glycosyltransferase, LthB. Although mutants with deletions of lthA, encoding another GT, and lthB were both defective for nanofibril formation, they exhibited different phenotypes of cell chain elongation and pellicle formation. Moreover, LthA expression, but not LthB expression, was influenced by extracellular calcium, which is known to affect nanofibril formation, indicating the functional diversities of LthA and LthB. Such molecular insights are critical for a better understanding of ecology of filamentous bacteria, which, in turn, can be used to improve strategies to control filamentous bacteria in industrial facilities.

Transcriptome and Deletion Mutant Analyses Revealed that an RpoH Family Sigma Factor Is Essential for Photosystem Production in Roseateles depolymerans under Carbon Starvation

Roseateles depolymerans is an obligately aerobic bacterium that produces a photosynthetic apparatus only under the scarcity of carbon substrates. We herein examined changes in the transcriptomes of R. depolymerans cells to clarify the expression of photosynthesis genes and their upstream regulatory factors under carbon starvation. Transcriptomes 0, 1, and 6‍ ‍h after the depletion of a carbon substrate indicated that transcripts showing the greatest variations (a 500-fold increase [6 h/0 h]) were light-harvesting proteins (PufA and PufB). Moreover, loci with more than 50-fold increases (6 h/0‍ ‍h) were fully related to the photosynthetic gene cluster. Among 13 sigma factor genes, the transcripts of a sigma 70 family sigma factor related to RpoH (SP70) increased along photosynthesis genes under starvation; therefore, a knockout experiment of SP70 was performed. ΔSP70 mutants were found to lack photosynthetic pigments (carotenoids and bacteriochlo-rophyll a) regardless of carbon starvation. We also examined the effects of heat stress on ΔSP70 mutants, and found that SP70 was also related to heat stress tolerance, similar to other RpoH sigma factors (while heat stress did not trigger photosystem production). The deficient accumulation of photosynthetic pigments and the heat stress tolerance of ΔSP70 mutants were both complemented by the introduction of an intact SP70 gene. Furthermore, the transcription of photosynthetic gene operons (puf, puh, and bch) was markedly reduced in the ΔSP70 mutant. The RpoH homologue SP70 was concluded to be a sigma factor that is essential for the transcription of photosynthetic gene operons in R. depolymerans.

Porous Pellicle Formation of a Filamentous Bacterium, Leptothrix

The bacterium Leptothrix cholodnii generates filaments encased in a sheath comprised of woven nanofibrils. In static liquid culture, L. cholodnii moves toward the air-liquid interface, where it forms porous pellicles. Observations of aggregation at the interface reveal that clusters consisting of only a few bacteria primarily grow by netting free cells. These growing clusters hierarchically enlarge through the random docking of other small clusters. We find that the bacteria swim using their polar flagellum toward the interface, where their sheath assists them in intertwining with others and thereby promotes the formation of small clusters. In contrast, sheathless hydrophobic mutant cells get stuck to the interface. We find that the nanofibril sheath is vital for robust pellicle formation as it lowers cell surface hydrophobicity by 60%, thereby reducing their adsorption and enabling cells to move toward and stick together at the air-liquid interface. IMPORTANCE Efficient and sustainable management of water resources is becoming a fundamental issue for supporting growing populations and for developing economic activity. Fundamental to this management is the treatment of wastewater. Microorganisms are the active component of activated sludge that is employed in the biodegradation process of many wastewater treatment facilities. However, uncontrolled growth of filamentous bacteria such as Sphaerotilus often results in filamentous bulking, lowering the efficiency of water treatment systems. To prevent this undesirable condition, strategies based on a fundamental understanding of the ecology of filamentous bacteria are required. Although the filamentous bacterium Leptothrix cholodnii, which is closely related to Sphaerotilus, is a minor inhabitant of activated sludge, its complete genome sequence is known, making gene manipulation relatively easy. Moreover, L. cholodnii generates porous pellicles under static conditions, which may be a characteristic of filamentous bulking. We show that both swimming motility and nanofibril-mediated air-liquid interface attachment are required for porous pellicle formation. These insights are critical for a better understanding of the characteristics of filamentous bulking and might improve strategies to control activated sludge.

Structural determination of the sheath-forming polysaccharide of Sphaerotilus montanus using thiopeptidoglycan lyase which recognizes the 1,4 linkage between α-d-GalN and β-d-GlcA

Sphaerotilus natans is a filamentous sheath-forming bacterium commonly found in activated sludge. Its sheath is assembled from a thiolic glycoconjugate called thiopeptidoglycan. S. montanus ATCC-BAA-2725 is a sheath-forming member of stream biofilms, and its sheath is morphologically similar to that of S. natans. However, it exhibits heat susceptibility, which distinguishes it from the S. natans sheath. In this study, chemical composition and solid-state NMR analyses suggest that the S. montanus sheath is free of cysteine, indicating that disulfide linkage is not mandatory for sheath formation. The S. montanus sheath was successfully solubilized by N-acetylation, allowing solution-state NMR analysis to determine the sugar sequence. The sheath was susceptible to thiopeptidoglycan lyase prepared from the thiopeptidoglycan-assimilating bacterium, Paenibacillus koleovorans. The reducing ends of the enzymatic digests were labeled with 4-aminobenzoic acid ethyl ester, followed by HPLC. Two derivatives were detected, and their structures were determined. We found that the sheath has no peptides and is assembled as follows: [→4)-β-d-GlcA-(1→4)-β-d-Glc-(1→3)-β-d-GalNAc-(1→4)-α-d-GalNAc-(1→4)-α-d-GalN-(1→]_n (β-d-Glc and α-d-GalNAc are stoichiometrically and substoichiometrically 3-O-acetylated, respectively). Thiopeptidoglycan lyase was thus confirmed to cleave the 1,4 linkage between α-d-GalN and β-d-GlcA, regardless of the peptide moiety. Furthermore, vital fluorescent staining of the sheath demonstrated that elongation takes place at the tips, as with the S. natans sheath.

Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform

Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02617-3.

Polyfunctional Nanofibril Appendages Mediate Attachment, Filamentation, and Filament Adaptability in Leptothrix cholodnii

Leptothrix is a species of Fe/Mn-oxidizing bacteria known to form long filaments composed of chains of cells that eventually produce a rigid tube surrounding the filament. Prior to the formation of this brittle microtube, Leptothrix cells secrete hair-like structures from the cell surface, called nanofibrils, which develop into a soft sheath that surrounds the filament. To clarify the role of nanofibrils in filament formation in L. cholodnii SP-6, we analyze the behavior of individual cells and multicellular filaments in high-aspect ratio microfluidic chambers using time-lapse and intermittent in situ fluorescent staining of nanofibrils, complemented with atmospheric scanning electron microscopy. We show that in SP-6 nanofibrils are important for attachment and their distribution on young filaments post-attachment is correlated to the directionality of filament elongation. Elongating filaments demonstrate a surprising ability to adapt to their physical environment by changing direction when they encounter obstacles: they bend or reverse direction depending on the angle of the collision. We show that the forces involved in the collision can be used to predict the behavior of filament. Finally, we show that as filaments grow in length, the older region becomes confined by the sheath, while the newly secreted nanofibrils at the leading edge of the filament form a loose, divergent, structure from which cells periodically escape.

Advanced biofilm analysis in streams receiving organic deicer runoff

Prolific heterotrophic biofilm growth is a common occurrence in airport receiving streams containing deicers and anti-icers, which are composed of low-molecular weight organic compounds. This study investigated biofilm spatiotemporal patterns and responses to concurrent and antecedent (i.e., preceding biofilm sampling) environmental conditions at stream sites upstream and downstream from Milwaukee Mitchell International Airport in Milwaukee, Wisconsin, during two deicing seasons (2009-2010; 2010-2011). Biofilm abundance and community composition were investigated along spatial and temporal gradients using field surveys and microarray analyses, respectively. Given the recognized role of Sphaerotilus in organically enriched environments, additional analyses were pursued to specifically characterize its abundance: a consensus sthA sequence was determined via comparison of whole metagenome sequences with a previously identified sthA sequence, the primers developed for this gene were used to characterize relative Sphaerotilus abundance using quantitative real-time PCR, and a Sphaerotilus strain was isolated to validate the determined sthA sequence. Results indicated that biofilm abundance was stimulated by elevated antecedent chemical oxygen demand concentrations, a surrogate for deicer concentrations, with minimal biofilm volumes observed when antecedent chemical oxygen demand concentrations remained below 48 mg/L. Biofilms were composed of diverse communities (including sheathed bacterium Thiothrix) whose composition appeared to shift in relation to antecedent temperature and chemical oxygen demand. The relative abundance of sthA correlated most strongly with heterotrophic biofilm volume (positive) and dissolved oxygen (negative), indicating that Sphaerotilus was likely a consistent biofilm member and thrived under low oxygen conditions. Additional investigations identified the isolate as a new strain of Sphaerotilus montanus (strain KMKE) able to use deicer components as carbon sources and found that stream dissolved oxygen concentrations related inversely to biofilm volume as well as to antecedent temperature and chemical oxygen demand. The airport setting provides insight into potential consequences of widescale adoption of organic deicers for roadway deicing.

Integrated effects of temperature and COD/N on an up-flow anaerobic filter-biological aerated filter: Performance, biofilm characteristics and microbial community

The integrated effects of temperature and COD/N ratio on performance, biofilm characteristics and microbial community in up-flow anaerobic filter-biological aerated filters (UAF-BAFs) were investigated. Results indicated that the UAF-BAF system could achieve excellent COD, NH₄⁺-N and TN removal, in which effluent quality well met the Class 1A standard. Biofilm physicochemical characteristics showed that the biomass, biofilm thickness and extracellular polymeric substance (EPS) content in the UAF-BAFs reduced with the decrease in COD/N ratio, but were enhanced under low temperature. The biofilm structure characterized by CLSM in the UAF-BAFs significantly shifted, which was closely correlated with operational conditions. Sequencing analysis revealed that Proteobacteria, Epsilonbacteraeota, Bacteroidetes and Firmicutes were dominant in the UAFs and the abundance of ammonium oxidizing bacteria (AOB) was responsible for nitrification performance in the BAFs. Functions analysis indicated that amino acid metabolism, carbohydrate metabolism, energy metabolism and lipid metabolism were clearly regulated by parameters changes.

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575^T under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575^T grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575^T are dominant under anoxic conditions. Furthermore, strain DSM 6575^T forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575^T, and could contribute to biogeochemical cycles of Fe and N in the environment.

Structure of perosamine-containing polysaccharide, a component of the sheath of Thiothrix fructosivorans

A sheath-forming and sulfur-oxidizing bacterium, Thiothrix fructosivorans, was heterotrophically cultured. The sheath, which is an extracellular microtube, was prepared by selectively removing the cells using lysozyme, sodium dodecyl sulfate, and sodium hydroxide. Solid-state (13)C-nuclear magnetic resonance (NMR) spectrum revealed that the sheath is assembled from a glycan possessing acetyl and methyl groups. When the sheath was deacetylated, the original microtube structure was lost and the sheath became soluble under acidic conditions, revealing the importance of acetyl groups in maintaining the sheath structure. Equimolar d-glucose, d-glucosamine, and l-fucose were detected in the acid hydrolysate of the sheath by gas liquid chromatography. In addition to these sugars, β-GlcN-(1→4)-Glc and unidentified sugar were detected by analyzing the hydrolysate using high-performance liquid chromatography analysis. (1)H and (13)C NMR spectroscopy was used to identify a disaccharide composed of 4-deoxy-4-aminorhamnose (perosamine, Rha4N) and fucose. N-Acetyl-perosamine prepared from the disaccharide was polarimetric and exhibited a d-configuration. The previously unidentified disaccharide was found to be α-d-Rhap4N-(1→3)-d-Fuc. According to (1)H and (13)C NMR analyses, the deacetylated sheath-forming polysaccharide was found to h have a main chain of [→4)-β-d-GlcpN-(1→4)-β-d-Glcp-(1→]n, to which disaccharide side chains of α-d-Rhap4N-(1→3)-α-l-Fucp-(1→ were attached at position 3 of Glc.

Analysis of bacterial community in bulking sludge using culture-dependent and -independent approaches

The bacterial community of a bulking sludge from a municipal wastewater treatment plant with anoxic-anaerobic-oxic process was investigated by combination of cultivation and 16S rRNA gene clone library analysis for understanding the causes of bulking. A total of 28 species were obtained from 63 isolates collected from six culture media. The most cultivable species belonged to gamma-Proteobacteria including Klebsiella sp., Pseudomonas sp., Aeromonas sp. and Acinetobacter sp. Further analysis of these strains by repetitive sequence based on polymerase chain reaction (rep-PCR) technology showed that rep-PCR yielded discriminatory banding patterns within the same genus using REP and BOX primer sets. While the culture-independent assessment revealed that beta-Proteobacteria was the dominant group in the bulking sample. Sequence analysis revealed that the highest proportion (14.7%) of operational taxonomic units was 98% similar to Candidatus Accumulibacter phosphatis, which is used to remove phosphorous from wastewater. Our results indicated that combining different approaches can produce complementary information, thus generate a more accurate view of microbial community in bulking sludge.

Reduction of hexavalent chromium by Sphaerotilus natans a filamentous micro-organism present in activated sludges

Wastewaters produced by various industries may contain undesirable amounts of hexavalent chromium (Cr(VI)), as chromate and dichromate, a hazardous metal affecting flora and animals of aquatic ecosystems as well as human health. One removal strategy comprises the microbial reduction of Cr(VI) to Cr(III), a less soluble chemical species that is less toxic than Cr(VI). In this work, the ability to reduce Cr(VI) of Sphaerotilus natans, a filamentous bacterium usually found in activated sludge systems, was evaluated. In aerobic conditions, S. natans was able to efficiently reduce Cr(VI) to Cr(III) from dichromate solutions ranging between 4.5 and 80 mg Cr(VI)l(-1) in the presence of a carbonaceous source. A simultaneous evaluation of the microbial respiratory activity inhibition was also carried out to analyze the toxic effect of Cr(VI). Cr(VI) reduction by S. natans was mathematically modeled; chromium(VI) reduction rate depended on both Cr(VI) concentration and active biomass concentration. Although it is known that S. natans removes heavy metal cations such as Cr(III) by biosorption, the ability of this micro-organism to reduce Cr(VI), which behaves as an oxyanion in aqueous solutions, is a novel finding. The distinctive capacity to reduce Cr(VI) to Cr(III) than remain soluble or precipitated becomes S. natans a potential micro-organism to decontaminate wastewaters.

Structural analysis of the sheath of a sheathed bacterium, Leptothrix cholodnii

Leptothrix cholodnii is an aerobic sheath-forming bacterium often found in oligotrophic and metal-rich aquatic environments. The sheath of this bacterium was isolated by selectively lysing the cells. Glycine and cysteine were the major amino acids of the sheath. The sheath was readily dissolved in hydrazine, and a polysaccharide substituted with cysteine was recovered from the solution. Galactosamine, glucosamine and galacturonic acid were detected in the hydrazinolysate by gas liquid chromatography analysis. FAB-MS analysis of the hydrazinolysate suggested a sugar sequence of HexN-GalA-HexN-HexN. Methylation linkage analysis revealed the presence of 4-linked GalA, 3-linked HexN and 4-linked HexN. The sulfhydryl groups of the sheath were used for labeling with the fluorogenic reagent, 4-(aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (ABD-F). The labeled sheath (ABD-sheath) was partially hydrolyzed and three fluorescent fragments were purified by HPLC. One of them was identified as ABD-cysteine. The second one was found to be the ABD-cysteine tetramer. Another fragment was indicated to be a pentasaccharide substituted with ABD-cysteine by nuclear magnetic resonance (NMR) analysis. It can be assumed that the polysaccharide and peptide moieties of the sheath are connected by a cysteine residue. NMR analysis of the hydrazinolysate revealed that the polysaccharide moiety of the sheath was constructed from a pentasaccharide repeating unit containing 2-amino-2-deoxygalacturonic acid (GalNA), as shown below. -->4)-alpha-GalNA-(1-->4)-alpha-D-GalN(p)-(1-->4)-alpha-D-GalA(p)-(1-->4)-beta-D-GlcN(p)-(1-->3)-beta-D-GalN(p)-(1-->.

Structure of the polysaccharide isolated from the sheath of Sphaerotilus natans

A polysaccharide was isolated from the sheath of a sheathed bacterium, Sphaerotilus natans. The sheath polysaccharide (SPS) was composed of D-glucose and D-(N-acetyl)galactosamine in molar ratios of 1:4. Methylation linkage analysis revealed the presence of the residues of 4-linked glucose, 4-linked (N-acetyl)galactosamine, and 3-linked (N-acetyl)galactosamine in molar ratios of 1:3:1. The oligomer of SPS was prepared with an SPS-specific degrading enzyme from a sheath-degrading bacterium, Paenibacillus koleovorans. The oligomer was derivatized and subjected to fast atom bombardment-mass spectrometry to investigate the monosaccharide sequence of SPS. The structure of SPS was confirmed by nuclear magnetic resonance. The resulting data showed that SPS is a straight-chained basic polysaccharide constructed of a pentasaccharide repeating unit.