Complete genome and phenotypic characterization of Zobellella denitrificans MW1 reveal carbon source preferences and a phosphate-associated shift in polyhydroxybutyrate accumulation.

Abstract

Zobellella denitrificans MW1 is a halotolerant, facultatively anaerobic bacterium with high poly(3-hydroxybutyrate) (PHB) productivity that lacked a complete genome sequence. Here we report its first complete circular genome (4.10 Mb, 63.6% GC), obtained by hybrid Illumina-Nanopore assembly, with multi-scale cultivation data. The genome encodes a conserved phaCAB operon, multiple sucrose uptake and catabolic systems, and a canonical Pho regulon with polyphosphate metabolism genes (ppk, ppx). Ten CRISPR arrays, an intact prophage and no acquired multidrug resistance determinants were identified. Carbohydrate utilization was broad yet selective: sucrose, glucose and fructose supported the highest biomass, sucrose yielding up to 76% PHB of cell dry weight (CDW) in flasks; sucrose-rich beet molasses sustained PHB accumulation in flasks and 5 L bioreactors. In single, non-replicated fed-batch runs, a high-phosphate process reached 23 g L⁻¹ CDW with minimal PHB, whereas a low-phosphate process reached 53 g L⁻¹ CDW with 78% PHB. Because each regime was run once, these data are observations rather than a statistically supported comparison. They suggest that phosphate availability may be an important variable governing the growth-versus-storage balance, and that sucrose-rich industrial side-streams can be converted into PHB. The genomic co-occurrence of the Pho regulon, polyphosphate metabolism and phaCAB offers a hypothesis that remains to be tested by expression, enzyme-activity and targeted genetic experiments. Overall, MW1 is established as a genomically resolved platform for PHB production from low-cost, sucrose-rich feedstocks under saline conditions.