scholarly journals Phylogenetic Distribution of Plastic-Degrading Microorganisms

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Victor Gambarini ◽  
Olga Pantos ◽  
Joanne M. Kingsbury ◽  
Louise Weaver ◽  
Kim M. Handley ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Diversity ◽  
Synthetic Polymers ◽  
Tree Of Life ◽  
Natural Polymer ◽  
Phylogenetic Distribution ◽  
Orthologous Genes ◽  
Microbial Genomes ◽  
Microbial Species ◽  
Plastic Degradation

ABSTRACT The number of plastic-degrading microorganisms reported is rapidly increasing, making it possible to explore the conservation and distribution of presumed plastic-degrading traits across the diverse microbial tree of life. Putative degraders of conventional high-molecular-weight polymers, including polyamide, polystyrene, polyvinylchloride, and polypropylene, are spread widely across bacterial and fungal branches of the tree of life, although evidence for plastic degradation by a majority of these taxa appears limited. In contrast, we found strong degradation evidence for the synthetic polymer polylactic acid (PLA), and the microbial species related to its degradation are phylogenetically conserved among the bacterial family Pseudonocardiaceae. We collated data on genes and enzymes related to the degradation of all types of plastic to identify 16,170 putative plastic degradation orthologs by mining publicly available microbial genomes. The plastic with the largest number of putative orthologs, 10,969, was the natural polymer polyhydroxybutyrate (PHB), followed by the synthetic polymers polyethylene terephthalate (PET) and polycaprolactone (PCL), with 8,233 and 6,809 orthologs, respectively. These orthologous genes were discovered in the genomes of 6,000 microbial species, and most of them are as yet not identified as plastic degraders. Furthermore, all these species belong to 12 different microbial phyla, of which just 7 phyla have reported degraders to date. We have centralized information on reported plastic-degrading microorganisms within an interactive and updatable phylogenetic tree and database to confirm the global and phylogenetic diversity of putative plastic-degrading taxa and provide new insights into the evolution of microbial plastic-degrading capabilities and avenues for future discovery. IMPORTANCE We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved. We found 16,170 putative plastic degradation orthologs in the genomes of 12 different phyla, which suggests a vast potential for the exploration of these traits in other taxa. Besides making the database available to the scientific community, we also created an interactive phylogenetic tree that can display all of the collated information, facilitating visualization and exploration of the data. Both the database and the tree are regularly updated to keep up with new scientific reports. We expect that our work will contribute to the field by increasing the understanding of the genetic diversity and evolution of microbial plastic-degrading traits.

scholarly journals Enzymes Involved in Plastic Degradation

2021 ◽  
pp. 95-110
Author(s):  
S.Z.Z. Cobongela
Keyword(s):  
Polyethylene Terephthalate ◽  
Synthetic Polymers ◽  
Chemical Degradation ◽  
Natural Resistance ◽  
Aquatic Life ◽  
Carbon Backbone ◽  
Catabolic Enzymes ◽  
Plastic Degradation ◽  
Global Increase ◽  
Physical And Chemical

The global increase in production of plastic and accumulation in the environment is becoming a major concern especially to the aquatic life. This is due to the natural resistance of plastic to both physical and chemical degradation. Lack of biodegradability of plastic polymers is linked to, amongst other factors, the mobility of the polymers in the crystalline part of the polyesters as they are responsible for enzyme interaction. There are significantly few catabolic enzymes that are active in breaking down polyesters which are the constituents of plastic. The synthetic polymers widely used in petroleum-based plastics include polyethylene (PE), polypropylene (PP), polyvinylchloride (PVC), polyurethane (PUR), polystyrene (PS), polyamide (PA) and polyethylene terephthalate (PET) being the ones used mostly. Polymers with heteroatomic backbone such as PET and PUR are easier to degrade than the straight carbon-carbon backbone polymers such as PE, PP, PS and PVC.

scholarly journals Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices

2018 ◽  
Vol 46 ◽  
pp. 192-198 ◽  
Author(s):  
Markus Gastauer ◽  
Cecílio Frois Caldeira ◽  
Ian Trotter ◽  
Silvio Junio Ramos ◽  
João Augusto Alves Meira Neto
Keyword(s):  
Phylogenetic Diversity ◽  
Tree Of Life ◽  
Dispersion Indices

Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 170-182 ◽  
Author(s):  
Mariam Adeoba ◽  
Solomon G. Tesfamichael ◽  
Kowiyou Yessoufou
Keyword(s):  
Threatened Species ◽  
Phylogenetic Diversity ◽  
Extinction Risk ◽  
Phylogenetic Signal ◽  
Distinct Species ◽  
Tree Of Life ◽  
Fish Family ◽  
The Face ◽  
Taxonomic Confusion ◽  
Coi Sequences

Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.

scholarly journals Phylogenetically informed spatial planning is required to conserve the mammalian tree of life

2017 ◽  
Vol 284 (1865) ◽  
pp. 20170627 ◽  
Author(s):  
Dan F. Rosauer ◽  
Laura J. Pollock ◽  
Simon Linke ◽  
Walter Jetz
Keyword(s):  
Conservation Planning ◽  
Phylogenetic Diversity ◽  
Informed Choice ◽  
Tree Of Life ◽  
Phylogenetic Information ◽  
Mammal Conservation ◽  
The Face ◽  
New Generation ◽  
The Impact ◽  
Effective Conservation

In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species. In many locations, priorities for PD differ substantially from those of a species-based approach that ignores evolutionary relationships. This discrepancy increases rapidly as the amount of land available for conservation declines, as does the relative benefit for mammal conservation (for the same area protected). This benefit is equivalent to an additional 5900 Myr of distinct mammalian evolution captured simply through a better informed choice of priority areas. Our study uses area targets for PD to generate more realistic conservation scenarios, and tests the impact of phylogenetic uncertainty when selecting areas to represent diversity across a phylogeny. It demonstrates the opportunity of using rapidly growing phylogenetic information in conservation planning and the readiness for a new generation of conservation planning applications that explicitly consider the heritage of the tree of life's biodiversity.

scholarly journals Preparation of Tannin Based Hydrogel for Biological Application

2011 ◽  
Vol 8 (4) ◽  
pp. 1638-1643 ◽  
Author(s):  
R. Jameel Mhessn ◽  
L. Abd-Alredha ◽  
R. Al-Rubaie ◽  
A. Fuad Khudair Aziz
Keyword(s):  
Diffusion Coefficient ◽  
Phenolic Compounds ◽  
Wound Dressing ◽  
Synthetic Polymers ◽  
Natural Polymer ◽  
Biological Application ◽  
Artificial Membrane ◽  
Polymeric Blends ◽  
Natural Phenolic Compounds ◽  
Diaphragm Cell

Polymeric blends as potential wound dressing were prepared. Natural polymer (Tannin) and synthetic polymers (PVA and PEG) were used to prepare heterogeneous blends. The product was identified by spectrophotometry. A diaphragm cell was used to measure the diffusion coefficient (D). The result shown the PEG-PVA disk was very faster permeability for all solution. The D of PVA/ PEG-Tannin blend was 0.184x10-3cm2/s higher than Tannin-PEG blend was 0.038x10-3cm2/s. The natural phenolic compounds that can be used artificial membrane to inhibit growth or kill microorganism such as bacteria or fungi.

scholarly journals Legume Symbiotic Nitrogen Fixation byβ-Proteobacteria Is Widespread inNature

2003 ◽  
Vol 185 (24) ◽  
pp. 7266-7272 ◽  
Author(s):  
Wen-Ming Chen ◽  
Lionel Moulin ◽  
Cyril Bontemps ◽  
Peter Vandamme ◽  
Gilles Béna ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nitrogen Fixation ◽  
Phylogenetic Tree ◽  
Phylogenetic Diversity ◽  
Symbiotic Nitrogen Fixation ◽  
The Other ◽  
Gene Sequences ◽  
Free Living ◽  
Initial Discovery ◽  
Different Strains

ABSTRACT Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the β-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating thatβ -proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial β-proteobacteria (β-rhizobia) are very similar to those of rhizobia from theα -subclass (α-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. Theβ -rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered β-rhizobial sequences in two nodA lineages intertwined with α-rhizobial sequences. On the other hand, theβ -rhizobia were grouped with free-living nitrogen-fixingβ -proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that β-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.

scholarly journals Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter!

2021 ◽  
Vol 4 ◽  
Author(s):  
Haris Zafeiropoulos ◽  
Laura Gargan ◽  
Christina Pavloudi ◽  
Evangelos Pafilis ◽  
Jens Carlsson
Keyword(s):  
Dark Matter ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Marker Gene ◽  
Environmental Dna ◽  
Tree Of Life ◽  
Taxonomic Assignment ◽  
Species Identity ◽  
Consensus Sequences ◽  
Coi Sequences

Environmental DNA (eDNA) metabarcoding has been commonly used in recent years (Jeunen et al. 2019) for the identification of the species composition of environmental samples. By making use of genetic markers anchored in conserved gene regions, universally present acrooss the species of large taxonomy groups, eDNA metabarcoding exploits both extra- and intra-cellular DNA fragments for biodiversity assessment. However, there is not a truly “universal” marker gene that is capable of amplifying all species across different taxa (Kress et al. 2015). The mitochondrial cytochrome C oxidase subunit I gene (COI) has many of the desirable properties of a “universal" marker and has been widely used for assessing species identity in Eukaryotes, especially metazoans (Andjar et al. 2018). However, a great number of COI Operational Taxonomic Units (OTUs) or/and Amplicon Sequence Variants (ASVs) retrieved from such studies do not match reference sequences and are often referred to as “dark matter” (Deagle et al. 2014). The aim of this study was to discover the origins and identities of these COI dark matter sequences. We built a reference phylogenetic tree that included as many COI-sequence-related information across the tree of life as possible. An overview of the steps followed is presented in Fig. 1a. Briefly, the Midori reference 2 database was used to retrieve eukaryotes sequences (183,330 species). In addition, the API of the BOLD database was used as source for the corresponding Bacteria (559 genera) and Archaea (41 genera) sequences. Consensus sequences at the family level were constructed from each of these three initial COI datasets. The COI-oriented reference phylogenetic tree of life was then built by using 1,240 consensus sequences with more than 80% of those coming from eukaryotic taxa. Phylogeny-based taxonomic assignment was then used to place query sequences. The a) total number of sequences, b) sequences assigned to Eukaryotes and c) unassigned subsets of OTUs, from marine and freshwater samples, retrieved during in-house metabarcoding experiments, were placed in the reference tree (Fig. 1b). It is clear that a large proportion of sequences targeting the COI region of Eukaryotes actually represents bacterial branches in the phylogenetic tree (Fig. 1b). We conclude that COI metabarcoding studies targeting Eukaryotes may come with a great bias derived from amplification and sequencing of bacterial taxa, depending on the primer pair used. However, for the time being, publicly available bacterial COI sequences are far too few to represent the bacterial variability; thus, a reliable taxonomic identification of them is not possible. We suggest that bacterial COI sequences should be included in the reference databases used for the taxonomy assignment of OTUs/ASVs in COI-based eukaryote metabarcoding studies to allow for bacterial sequences that were amplified to be excluded enabling researchers to exclude non-target sequences. Further, the approach presented here allows researchers to better understand the unknown unknowns and shed light on the dark matter of their metabarcoding sequence data.

scholarly journals The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes

2019 ◽  
Author(s):  
Maria A. Sierra ◽  
Chandrima Bhattacharya ◽  
Krista Ryon ◽  
Sophie Meierovich ◽  
Heba Shaaban ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Gram Stain ◽  
Microbial Genomes ◽  
Resistance To Antibiotics ◽  
Microbial Species ◽  
Gene Annotations ◽  
Comprehensive Database ◽  
Broad Community

AbstractThe Microbe Directory (TMD) is a comprehensive database of annotations for microbial species collating features such as gram-stain, capsid-symmetry, resistance to antibiotics and more. This work presents a significant improvement to the original Microbe Directory (2018). This update adds 68,852 taxa, many new annotation features, an interface for the statistical analysis of microbiomes based on TMD features, and presents a portal for the broad community to add or correct entries. This update also adds curated lists of gene annotations which are useful for characterizing microbial genomes. Much of the new data in TMD is sourced from a set of databases and independent studies collating these data into a single quality controlled and curated source. This will allow researchers and clinicians to have easier access to microbial data and provide for the possibility of serendipitous discovery of otherwise unexpected trends.

scholarly journals Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

2015 ◽  
Author(s):  
Jennifer Fouquier ◽  
Jai R Rideout ◽  
Evan Bolyen ◽  
John H Chase ◽  
Arron Shiffer ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Marker ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Sequence Data ◽  
Fungal Species ◽  
Bioinformatics Tool ◽  
Hybrid Gene ◽  
Fungal Database ◽  
Taxonomic Groups

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

Sign in / Sign up

Export Citation Format

Share Document