Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia

Neiella litorisoli sp. nov., an alginate lyase: producing bacterium from South China Sea, and proposal of Echinimonadaceae fam. nov. in the order Alteromonadales

A Gram-stain-negative, rod-shaped bacterium, designated HB171785^T, was isolated from soil sample collected from Qishui Bay, Hainan, China. The strain grew optimally at pH 7-8, 37-40 °C and with NaCl 3-4%. The predominant isoprenoid quinone was found to be Q-8 and the major fatty acids were C_16:0, C_16:1 ω7c/C_16:1 ω6c, C_18:1 ω7c/C_18:1 ω6c and C_12:0 3OH. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The size of the draft genome was 4.32 Mbp with G + C content 49.7%. Phylogenetic analysis of 16S rRNA gene sequence indicated that the closest phylogenetically related species were Neiella marina j221^T, "Neiella holothuriorum" 126 and Echinimonas agarilytica KMM 6351^T with the similarities of 98.2, 96.0 and 95.0%, respectively. The phylogenetic tree based on 16S rRNA gene and phylogenomic tree based on core genome showed that strain HB171785^T clustered together with N. marina j221^T, with the highest values of average nucleotide identity (82.9%) and digital DNA-DNA hybridization (25.4%). The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB171785^T represents a novel species of the genus Neiella, for which the name Neiella litorisoli sp. nov. is proposed. The type strain is HB171785^T (= MCCC 1K04625^T = KCTC 82319^T). In addition, Echinimonadaceae fam. nov. in the order Alteromonadales was proposed.

Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders

Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans Dsij^T has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4^T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.

Genome Analysis of a Novel Polysaccharide-Degrading Bacterium Paenibacillus algicola and Determination of Alginate Lyases

Carbohydrate-active enzymes (CAZymes) are an important characteristic of bacteria in marine systems. We herein describe the CAZymes of Paenibacillus algicola HB172198^T, a novel type species isolated from brown algae in Qishui Bay, Hainan, China. The genome of strain HB172198^T is a 4,475,055 bp circular chromosome with an average GC content of 51.2%. Analysis of the nucleotide sequences of the predicted genes shows that strain HB172198^T encodes 191 CAZymes. Abundant putative enzymes involved in the degradation of polysaccharides were identified, such as alginate lyase, agarase, carrageenase, xanthanase, xylanase, amylases, cellulase, chitinase, fucosidase and glucanase. Four of the putative polysaccharide lyases from families 7, 15 and 38 were involved in alginate degradation. The alginate lyases of strain HB172198^T exhibited the maximum activity 152 U/mL at 50 °C and pH 8.0, and were relatively stable at pH 7.0 and temperatures lower than 40 °C. The average degree of polymerization (DP) of the sodium alginate oligosaccharide (AOS) degraded by the partially purified alginate lyases remained around 14.2, and the thin layer chromatography (TCL) analysis indicated that it contained DP2-DP8 oligosaccharides. The complete genome sequence of P. algicola HB172198^T will enrich our knowledge of the mechanism of polysaccharide lyase production and provide insights into its potential applications in the degradation of polysaccharides such as alginate.

Zobellia barbeyronii sp. nov., a New Member of the Family Flavobacteriaceae, Isolated from Seaweed, and Emended Description of the Species Z. amurskyensis, Z. laminariae, Z. russellii and Z. uliginosa

Six Gram-stain-negative, aerobic, rod-shaped, and motile by gliding bacterial strains were isolated from Pacific green and red algae. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel strains into the genus Zobellia as a distinct evolutionary lineage close to Zobellia nedashkovskayae Asnod2-B07-BT and Zobellia laminariae KMM 3676T sharing the highest similarity of 99.7% and 99.5%, respectively. The average nucleotide identity and the average amino acid identity values between strains 36-CHABK-3-33T and Z. nedashkovskayae Asnod2-B07-BT and Z. laminariae KMM 3676T were 89.7%/92.9% and 94.2%/95.8%, respectively. The digital DNA–DNA hybridization values based on the draft genomes between strains 36-CHABK-3-33T and Z. nedashovskayae Asnod2-B07-BT and Z. laminariae KMM 3676T were 39.5 ± 2.5% and 59.6 ± 2.7%, respectively. Multilocus sequence analysis based on house-keeping genes (dnaK, gyrB, pyrH, recA and topA) assigned the alga-associated isolates to the same species, which clustered separately from the recognized species of the genus Zobellia. The strains under study grew at 4–32 °C and with 0.5–8% NaCl and decomposed aesculin, gelatin, DNA, and Tweens 20 and 80, and weakly agar. The DNA G+C content was 36.7% calculated from genome sequence analysis for the strain 36-CHABK-3-33T. The predominant fatty acids of strain 36-CHABK-3-33T (>5% of the total fatty acids) were iso-C17:0 3-OH, summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH fatty acids), iso-C15:0, iso-C15:1 G, and C15:0. The major polar lipids were phosphatidylethanolamine, three unidentified lipids, and two unidentified aminolipids. The only detected respiratory quinone was MK-6. The significant molecular distinctiveness between the novel isolates and their nearest neighbor was strongly supported by differences in physiological and biochemical tests. Therefore, the six novel strains represent a novel species of the genus Zobellia, for which the name Zobellia barbeyronii sp. nov. is proposed. The type strain is 36-CHABK-3-33T (= KACC 21790T = KMM 6746T).