Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other plastics has become a severe global ...problem. Here, we report on the polyester degrading ability of a novel carboxylic ester hydrolase identified in the genome of the marine hydrocarbonoclastic bacterium
VGXO14
. The enzyme, designated PE-H, belongs to the type IIa family of PET hydrolytic enzymes as indicated by amino acid sequence homology. It was produced in
, purified and its crystal structure was solved at 1.09 Å resolution representing the first structure of a type IIa PET hydrolytic enzyme. The structure shows a typical α/β-hydrolase fold and high structural homology to known polyester hydrolases. PET hydrolysis was detected at 30°C with amorphous PET film (PETa), but not with PET film from a commercial PET bottle (PETb). A rational mutagenesis study to improve the PET degrading potential of PE-H yielded variant PE-H (Y250S) which showed improved activity, ultimately also allowing the hydrolysis of PETb. The crystal structure of this variant solved at 1.35 Å resolution allowed to rationalize the improvement of enzymatic activity. A PET oligomer binding model was proposed by molecular docking computations. Our results indicate a significant potential of the marine bacterium
for PET degradation.
A highly lead(II) resistant (up to 2200 mg/l) bacterium PbRPSD202 was selected among 210 lead resistant bacteria isolated from marine environment of Paradeep Port, Odisha for possible biosoption of ...toxic Pb (II) ions from metals polluted environments. The bacterium was identified as Bacillus xiamenensis following the phenotypic as well as 16S rRNA gene sequence analysis. In addition to Pb(II), it also showed resistance towards other heavy metals like Cd(II), Cr(VI), As(III), Cu(II), Ni(II) and Zn(II). Batch biosorption of Pb(II) using both live and dead biomass of this strain was investigated under different operational parametric conditions such as pH, temperature, NaCl concentration, shaking speed, treatment time, biomass concentration and initial Pb(II) concentration. The maximum Pb(II) uptake of 216.75 and 207.4 mg/g biomass was obtained with live and dead biomass, respectively, at the optimum condition (4% w/v NaCl, pH 6.0, 35 °C, 140 rpm and 1 g/l biosorbent dose). Both active as well as passive Pb(II) bio-sorption process showed best fit with the pseudo-second-order kinetic model. The sorption mechanism was favoured with Langmuir isotherm model indicating monolayer type adsorption. FTIR and FESEM-EDX analysis further ensured the possible interactions of Pb(II) with bacterial cell surface ligands like hydroxyl, carbonyl, carboxyl and amine groups during surface adsorption. TEM analysis revealed the intracellular accumulation of lead ions. This investigation highlights the potential application of this bacterium for bioremediation of lead(II) from the multiple metals contaminated saline environment through biosorption.
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•Isolated B. xiamenensis PbRPSD202 is a noble marine Pb(II) resistant bacterium.•This strain is also found to be an efficient multiple metal resistant bacteria.•Isotherm study ensured the effective loading of Pb(II) on the bacterial biomass.•Maximum Pb(II) loading capacity of live and dead biomass was 216.75 and 207.4 mg/g.•TEM & SEM analysis ascertained the extra- and intra-cellular accumulation of Pb(II).
The deep ocean is the largest marine environment on Earth and is home to a large reservoir of biodiversity. Within the deep ocean, large organic falls attract a suite of metazoans and microorganisms, ...which form an important community that, in part, relies on reduced chemical compounds. Here, we describe a deep-sea (4204m) microbial community associated with sediments collected underneath a whale fall skeleton in the South Atlantic Ocean. Metagenomic analysis of 1Gb of Illumina HiSeq. 2000 reads, including taxonomic and functional genes, was performed by using the MG-RAST pipeline, SEED, COG and the KEGG database. The results showed that Proteobacteria (79%) was the main phylum represented. The most dominant bacterial class in this phylum was Epsilonproteobacteria (69%), and Sulfurovum sp. NBC37-1 (97%) was the dominant species. Different species of Epsilonproteobacteria have been described in marine and terrestrial environments as important organisms for nutrient cycling. Functional analysis revealed key genes for nitrogen and sulfur cycles, including protein sequences for Sox system (sulfur oxidation) enzymes. These enzymes were mainly those of the Epsilonproteobacteria, indicating their importance for nitrogen and sulfur cycles and the balance of nutrients in this environment.
Biofilm-forming bacteria adhere to the substrates and engage in the nutrient cycling process. However, environmental conditions may interrupt the biofilm formation ability, which ultimately may ...affect various biogeochemical cycles. The present study reports the effect of varying pH and subsequent change in pCO2 on the survivability, biofilm formation, and synthesis of extracellular polymeric substances (EPS) of a biofilm-forming marine bacterium Bacillus stercoris GST-03 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India. Understanding the pH-dependent alteration in EPS constituents, and associated functional groups of a marine bacterium will provide better insight into the adaptability of the bacteria in future ocean acidification scenarios. The strain was found to tolerate and form biofilm up to pH 4, with the maximum biofilm formation at pH 6. EPS yield and the synthesis of the key components of the EPS, including carbohydrate, protein, and lipid, were found maximum at pH 6. Changes in biofilm formation patterns and various topological parameters at varying pH/pCO2 conditions were observed. A cellular chaining pattern was observed at pH 4, and maximum biofilm formation was obtained at pH 6 with biomass of 5.28582 ± 0.5372 μm3/μm2 and thickness of 9.982 ± 1.5288 μm. Structural characterization of EPS showed changes in various functional groups of constituent macromolecules with varying pH. The amorphous nature of the EPS and the changes in linkages and associated functional groups (-R2CHOR, –CH3, and –CH2) with pH variation was confirmed. EPS showed a two-step degradation with a maximum weight loss of 59.147% and thermal stability up to 480 °C at pH 6. The present work efficiently demonstrates the role of EPS in providing structural and functional stability to the biofilm in varying pH conditions. The findings will provide a better understanding of the adaptability of marine bacteria in the future effect of ocean acidification.
Using the OSMAC (One Strain Many Compounds) approach, the actinobacterium Streptomyces griseorubiginosus, derived from an unidentified cnidarian collected from a reef near Pointe de Bellevue in ...Réunion Island (France), was subjected to cultivation under diverse conditions. This endeavour yielded the isolation of a repertoire of 23 secondary metabolites (1–23), wherein five compounds were unprecedented as natural products (19–23). Specifically, compounds 19 and 20 showcased novel anthrone backbones, while compound 23 displayed a distinctive tetralone structure. Additionally, compounds 21 and 22 presented an unusual naphtho 2,3-cfuran-4(9H)-one chromophore. Interestingly, the detection of all these novel compounds (19–23) was exclusively achieved when the bacterium was cultured in FA-1 liquid medium supplemented with the epigenetic modifier γ-butyrolactone. The elucidation of the structural features of the newfound compounds was accomplished through a combination of HRESIMS, 1D and 2D NMR spectroscopy, as well as QM-NMR (Quantum Mechanical—Nuclear Magnetic Resonance) methods and by comparison with existing literature. Moreover, the determination of the relative configuration of compound 23 was facilitated by employing the mix-J-DP4 computational approach.
Xylans are polysaccharides composed of xylose and include β1,4-xylan, β1,3-xylan, and β1,3/1,4-mixed-linkage xylan (MLX). MLX is widely present in marine red algae and constitutes a significant ...organic carbon in the ocean. Xylanases are hydrolase enzymes that play an important role in xylan degradation. While a variety of β1,4-xylanases and β1,3-xylanases involved in the degradation of β1,4-xylan and β1,3-xylan have been reported, no specific enzyme has yet been identified that degrades MLX. Herein, we report the characterization of a new MLX-specific xylanase from the marine bacterium Polaribacter sp. Q13 which utilizes MLX for growth. The bacterium secretes xylanases to degrade MLX, among which is Xyn26A, an MLX-specific xylanase that shows low sequence similarities (<27%) to β1,3-xylanases in the glycoside hydrolase family 26 (GH26). We show that Xyn26A attacks MLX precisely at β1,4-linkages, following a β1,3-linkage toward the reducing end. We confirm that Xyn26A and its homologs have the same specificity and mode of action on MLX, and thus represent a new xylanase group which we term as MLXases. We further solved the structure of a representative MLXase, AlXyn26A. Structural and biochemical analyses revealed that the specificity of MLXases depends critically on a precisely positioned β1,3-linkage at the −2/−1 subsite. Compared to the GH26 β1,3-xylanases, we found MLXases have evolved a tunnel-shaped cavity that is fine-tuned to specifically recognize and hydrolyze MLX. Overall, this study offers a foremost insight into MLXases, shedding light on the biochemical mechanism of bacterial degradation of MLX.
Polyethylene (PE) is one of the most widespread plastic materials. Nevertheless, due to its recalcitrance against biological degradation and the presence of toxic additives, landfilled and carelessly ...disposed PE products have caused serious pollution in the natural environments. In this work, we aimed to investigate the growth characteristics of Microbulbifer hydrolyticus IRE-31 and its application in the biological degradation of low-density PE. The IRE-31 strain was isolated from marine pulp mill wastes rich in lignin which is a natural complex polymer containing also saturated carbon-carbon bonds like in PE. Following 30 days cultivation of the IRE-31 strain, the biodegradation of linear low-density PE particles was evidenced clearly by morphological changes of the polymer surface monitored by scanning electron microscopy and the formation of additional carbonyl groups in the polymer chains indicated by Fourier transform infrared spectroscopy.
•The degradation of polyethylene by a marine strain Microbulbifer hydrolyticus IRE-31 was observed by SEM and FTIR analysis.•The marine bacteria M. hydrolyticus IRE-31 shows potential to break down plastics in the ocean.•Phylogenetic analysis of M. hydrolyticus IRE-31 shows a close relationship with several known plastic degrading bacteria.
The endemic spread of plastic in the environment requires urgent need of a sustainable approach. Marine microbes found to have vast bioactivity and play a central role in biogeochemical cycling in ...the ocean; however, very few of them had been explored for biochemical cycling or plastic degradation. In the present study, we report the draft genome sequence of marine Bacillus sp. AIIW2 which was found to utilize plastic as a carbon source. The Bacillus sonorensis SRCM101395 was used as a reference genome for mapping the reads. The genome size of strain AIIW2 was approximately 4.4 Mb and composed of 4737 coding sequences with 45.7% G + C contents. The whole genome comparison of strain AIIW2 with three closest Bacillus strains showed strain specificity, the 16S ribosomal RNA sequence shows 99.93% similarity with Bacillus paralicheniformis KJ‐16T (KY694465). This genome data would provide the genetic basis in developing plastic bioremediation approaches and discover the enzymes pertinent in the biodegradation processes.
Carbohydrates are the product of carbon dioxide fixation by algae in the ocean. Their polysaccharides are depolymerized by marine bacteria, with a vast array of carbohydrate-active enzymes. These ...enzymes are important tools to establish biotechnological processes based on algal biomass. Green tides, which cover coastal areas with huge amounts of algae from the genus Ulva, represent a globally rising problem, but also an opportunity because their biomass could be used in biorefinery processes. One major component of their cell walls is the anionic polysaccharide ulvan for which the enzymatic depolymerization remains largely unknown. Ulvan lyases catalyze the initial depolymerization step of this polysaccharide, but only a few of these enzymes have been described. Here, we report the cloning, overexpression, purification, and detailed biochemical characterization of the endolytic ulvan lyase from Formosa agariphila KMM 3901.sup.T which is a member of the polysaccharide lyase family PL28. The identified biochemical parameters of the ulvan lyase reflect adaptation to the temperate ocean where the bacterium was isolated from a macroalgal surface. The NaCl concentration has a high influence on the turnover number of the enzyme and the affinity to ulvan. Divalent cations were shown to be essential for enzyme activity with Ca.sup.2+ likely being the native cofactor of the ulvan lyase. This study contributes to the understanding of ulvan lyases, which will be useful for future biorefinery applications of the abundant marine polysaccharide ulvan.
Most literature exploring the biological effects of ocean acidification (OA) has focused on macroscopic organisms and far less is known about how marine microbial communities will respond. Studies of ...OA and microbial community composition and diversity have examined communities from a limited number of ocean regions where the ambient pH is near or above the global average. At San Juan Island (Salish Sea), a region that experiences naturally low pH (average = 7.8), the picoplankton (cell diameter is 0.2-2mum) community was predicted to show no response to experimental acidification in a three-week mesocosm experiment. Filtered seawater mesocosms were maintained via semicontinuous culturing. Three control mesocosms were maintained at pH 8.05 and three acidified mesocosms were maintained at pH 7.60. Total bacteria was quantified daily with a flow cytometer. Microbial communities were sampled every two days via filtration followed by DNA extraction, 16S rRNA amplification, and MiSeq sequencing. There was no significant difference in total bacteria between pH treatments throughout the experiment. Acidification significantly reduced Shannon's diversity over time. During the final week of the experiment, acidification resulted in a significant decrease in Shannon's diversity, Faith's phylogenetic distance, and Pielous's Evenness. ANCOM results revealed four bacterial ASVs (amplicon sequence variants), in families Flavobaceriaceae and Hyphomonadaceae that significantly decreased in relative frequency under acidification and two bacterial ASVs, in families Flavobacteriaceae and Alteromonadaceae, that significantly increased under acidification. This is the first OA study on the microbial community of the Salish Sea, a nutrient rich, low pH region, and the first of its kind to report a decrease in both picoplankton richness and evenness with acidification. These findings demonstrate that marine microbial communities that naturally experience acidic conditions are still sensitive to acidification.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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