Biology subjects

Borchert, E.

Publications and source records attributed to Borchert, E..

5 recordsLinked to original sources

bioRxiv2025

A third type of PETase from the marine Halopseudomonas lineage

The enzymatic degradation of polyethylene terephthalate (PET) offers a sustainable solution for PET recycling. Over the past two decades, more than 100 PETases have been characterized, primarily exhibiting similar sequences and structures. Here, we report new PET-degrading /{beta} hydrolases, including HaloPETase1 from the marine Halopseudomonas lineage, thereby extending the narrow sequence space by novel features at the active site. The crystal structure of HaloPETase1 was determined to a resolution of 1.16 [A], revealing a unique active site architecture and a lack of the canonical {pi}-stacking clamp found in PETases so far. Further, variations in active site composition and loop structures were observed. Additionally, we found five more enzymes from the same lineage, two of which have a high similarity to type IIa bacterial PETases, while the other three resemble HaloPETase1. All these enzymes exhibited high salt tolerance ranging from 2.5 to 5 M NaCl leading to higher total product releases upon PET degradation at 40 or 50 {degrees}C. Based on these findings, we propose an extension of the existing PETase classification system to include type III PETases.

biochemistry↗

bioRxiv2024

Metagenomic analyses of the plastisphere reveals a common functional potential across oceans

Trillions of plastic particles have accumulated in the oceans, covered by microbial biofilms (termed the "plastisphere") whose functional potential remains unexplored. We evaluated genome-resolved bacterial metagenomes of the plastisphere from the North Atlantic and North Pacific garbage patches and compared their structure and functional potential to ambient plankton. Our data revealed a characteristic genetic potential of the plastisphere with functionally equivalent taxonomic units across both oceans. We found fewer coding genes, smaller genome sizes and lower GC-content in plankton in comparison to the plastisphere, despite residing in the same environment, reflecting a greater nutrient demand in the plastisphere. A functional gene analysis confirmed that the plastisphere consists of microorganisms with a higher potential to control their nutrient supply, metabolize a wider range of carbon sources, attenuate free radicals and use alternative energy sources like anoxygenic photosynthesis. Our results suggest that the overriding factor for the high functional similarity of the plastisphere in both oceans is the habitat for biofilm formation with the potential to support mutualism and nutrient sharing making genomic streamlining as found in plankton, unnecessary. Consequently, increasing plastic pollution promotes the expansion of new functional units within oligotrophic oceans, with the potential to impact biogeochemical cycles.

microbiology↗

bioRxiv2023

Maribacter halichondris sp. nov., isolated from the marine sponge Halichondria panicea

A new member of the family Flavobacteriaceae (termed Hal144T) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018 at Schilksee which is located in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the full-length Hal144T 16S rRNA gene sequence revealed similarities from 94.3% - 96.6% to the nearest type strains of the genus Maribacter. The phylogenetic tree depicted a cluster of strain Hal144T with its closest relatives Maribacter aestuarii GY20T (96.6%) and Maribacter thermophilus HT7-2T (96.3%). Genome comparisons of strain Hal144T with Maribacter spp. type strains exhibited average nucleotide identities in the range of 75% - 76% and digital DNA-DNA hybridization values in the range of 13.1% - 13.4%. Strain Hal144T was determined to be Gram-negative, mesophilic, strictly aerobic, flexirubin positive, resistant to aminoglycoside antibiotics, and able to utilize N-acetyl-{beta}-D-glucosamine. Optimal growth occurred at 25 - 30 {degrees}C, within a salinity range of 2 - 6% sea salt, and a pH range between 5 - 8. The major fatty acids identified were C17:0 3-OH, iso-C15:0, and iso-C15:1 G. The DNA G+C content of strain Hal144T was 41.4 mol%. Based on the polyphasic approach, strain Hal144T represents a novel species of the genus Maribacter, and we propose the name Maribacter halichondris sp. nov.. The type strain is Hal144T (= DSM 114563T = LMG 32744T).

microbiology↗

bioRxiv2022

16s rRNA gene sequence analysis of the microbial community on microplastic samples from the North Atlantic and Great Pacific Garbage Patches

The exponential increase in plastic production has led to their accumulation in the environment, particularly in oceans, polluting these environments from the shore to the open ocean and even sea ice in the pole regions. We compared microbial communities on plastic particles, known as "Plastisphere", collected from the Atlantic and Pacific oceans gyres in the Summer of 2019 and subsequently looked for potential plastic degraders. We applied a 16S rRNA amplicon sequencing approach to decipher differences and similarities in colonization behaviour between these two gyres. Two polymer types include plastics: polyethylene (PE) and polypropylene (PP). We found that microbes differed significantly between the two oceans and identified thirty-two differentially abundant taxa at the class level. Proteobacteria, Cyanobacteria and Bacteroidota were the most prominent relative abundant phyla in the two oceans. Finally, according to the current literature, we found 40 genera documented as potential plastic degraders. This study highlights the importance of the biogeographical location with respect to microbial colonization patterns of marine plastic debris, differing even in the open oceans. Furthermore, the wide distribution of potential plastic-degrading bacteria was shown.

bioinformatics↗

bioRxiv2020

Deciphering a marine bone degrading microbiome reveals a complex community effort

The marine bone biome is a complex assemblage of macro- and microorganisms, however the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from twelve relevant enzymatic families pertaining to collagenases, peptidases, glycosidases putatively involved in bone degradation were identified. Metagenome assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia. ImportanceBones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation marine environment. We herein demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.

microbiology↗