Enrichment of polyphenol metabolism within the ubiquitous SAR116 ‘Puniceispirillales’ bacterioplankton

Genomics and biogeography of novel Trichodesmium isolates from the Sargasso Sea

The cyanobacterium Trichodesmium is important in ocean nitrogen (N) and carbon (C) biogeochemistry through fixation of N2 gas and CO2 into NH3, amino acids, and carbohydrates. These essential compounds then fuel primary productivity, bacterial and grazing communities, and upper trophic levels. In the oligotrophic surface oceans, they are one of few taxa capable of utilizing both atmospheric C and N. Trichodesmium fall into 2 diazotrophic phylogenomic clades named “Thieb” and “Tery” after the most well characterized botanical species, Trichodesmium thiebautii and Trichodesmium erythraeum. Thieb is commonly the most abundant clade in all major ocean regions and paradoxically, is also the least characterized in terms of morphology, genomics, and ecophysiology due to underrepresentation in culture collections. In this study, 25 novel strains of Thieb were enriched in culture from the Sargasso Sea, phenotypically characterized, and whole genome sequenced. Cultures were found to belong to four well-supported subclades (i.e., ThiebA, ThiebB, ThiebC, and ThiebD). Trichodesmium subclades were found to have environmentally relevant differences in colony shape, gene content, cell dimensions, and inferred temperature range. Specifically, ThiebD and ThiebC had the largest biovolumes whereas ThiebA and ThiebB had the smallest. Importantly ThiebB also became relatively more abundant only in bulk seawater metagenomes collected at high temperature (>28°C). This finding indicates that as ocean warming continues, there may be shifts in Trichodesmium community structure towards smaller cells, which would affect overall C+N standing stocks.

Animal degradation of microbial storage polyhydroxyalkanoates.

A wide range of microorganisms produce storage biopolymer polyhydroxyalkanoates (sPHAs) as carbon and energy reserves. However, only bacteria and fungi are known to degrade microbial sPHAs, using enzymes called polyhydroxyalkanoate depolymerases (PHADs). Here we show that some animals also have PHADs that can degrade sPHAs. We discovered a PHAD in the gutless oligochaete Olavius algarvensis, a marine worm that gains nutrition by digesting bacterial symbionts, including a dominant symbiont in which sPHAs account for up to 42% of cellular carbon stores. Enzyme assays, combined with mass spectrometry, confirmed that heterologously expressed O. algarvensis PHAD degraded sPHAs into hydroxyalkanoate monomers that can enter conserved metabolic pathways. Imaging of mRNA showed that PHAD was expressed in the oligochaete epidermis, the site of symbiont digestion. We further identified PHADs in more than 66 gut-bearing animal species from nine phyla and 19 protist species from three major supergroups, suggesting that the last common ancestor of metazoans possessed PHADs. Functional assays confirmed that PHADs from phylogenetically distant animal lineages spanning aquatic and terrestrial environments degrade sPHAs. These findings reveal a previously unrecognized pathway by which protists and animals can access microbial carbon reserves, with broad relevance given the widespread occurrence of sPHAs across ecosystems.

Marine bacteria and fungi: the hidden treasure of oceans in the biodegradation of microplastics and hydrocarbons integrated with omics technologies.

Interactions between a Methanogenic Archaeon and Synthetic Musk Tonalide: A Balance of Cellular Inhibition and Detoxifying Biotransformation

The widespread use of synthetic musks, such as tonalide (AHTN), has led to their accumulation in anaerobic environments, such as sludge and sediments, raising concerns about their ecological impact. While methanogenic archaea are key ecological players in these environments, their responses to synthetic musks remain poorly understood. This study provides a systematic investigation of the interaction between AHTN and model methanogenic archaeon Methanosarcina acetivorans C2A. We found that AHTN toxicity is dependent on concentration, with 2 mg/L significantly inhibiting methanogenesis and growth by inducing oxidative stress and compromising cell membrane integrity. Despite this effect, M. acetivorans C2A was found to partially biotransform AHTN, achieving a value of 17.75% within 36 h. Using GC-MS/MS, six mono- and dihydroxylated metabolites were tentatively identified, indicating oxidation as the primary transformation mechanism. Notably, ecotoxicity modeling (ECOSAR) predicted these metabolites to be substantially less toxic than the parent AHTN, suggesting that this biotransformation is a detoxification pathway. These findings present the first evidence of archaeally mediated biotransformation of AHTN, revealing a dual role for methanogens as both targets of pollution and active agents in its natural attenuation.

Early-stage adaptation of pristine soil microbiota to Tetrabromobisphenol A: Unveiling rapid succession and ecophysiological mechanisms.

Addressing the limitations of existing studies that predominantly isolate Tetrabromobisphenol A (TBBPA)-degrading bacteria from contaminated environments and focus on degradation characteristics, this study employed multi-omics approaches to systematically elucidate the dynamic succession patterns and metabolic adaptation mechanisms of microbial communities from pristine soil under acute TBBPA stress, and achieved rapid screening of functional degraders. The results showed that TBBPA concentration and exposure time jointly drove community structural reconstruction, in which Methylobacillus and Pannonibacter, owing to their strong tolerance and high abundance, emerged as potential core degraders. Functional analysis indicated that high-concentration TBBPA (200 mg/L) reduced the abundance of the DLD gene by nearly 60%, whereas the community effectively alleviated energy metabolism inhibition through upregulation of upstream tricarboxylic acid cycle genes (CS, IDH3, and ACO) and respiratory chain functional genes (ccoN and ccoO), and formed a more tightly connected interaction network to enhance functional synergy. Metabolomic analysis revealed significant accumulation of membrane repair-related lipids (Gpetn and Lysopa) and amino acids (Norleucine and L-Phenylalanine), while pathways related to ABC transporters were activated, jointly confirming a stress adaptation mechanism centered on membrane repair and defense responses in the microbial community. The degradation process exhibited a multi-enzyme synergistic characteristic, with glutathione S-transferase playing a dominant role. After acclimation, the degradation efficiency of the microbial community was significantly improved, and the key strain Acinetobacter sp. T3 was successfully isolated. This study provides a theoretical basis and soil microbial communities for the development of in situ bioremediation technologies targeting persistent organic pollutants (POPs).

Surfactin-like lipopeptides contribute to interference competition of Bacillus velezensis against the marine Flavobacteriaceae in phycosphere.

This study demonstrates that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species.