Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes

The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.

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Potential for mcl-PHA production from nonanoic and azelaic acids

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0554 ◽

2018 ◽

Vol 64 (1) ◽

pp. 11-19 ◽

Cited By ~ 3

Author(s):

James Gillis ◽

Kenton Ko ◽

Juliana A. Ramsay ◽

Bruce A. Ramsay

Keyword(s):

Fatty Acids ◽

Oleic Acid ◽

Pseudomonas Fluorescens ◽

De Novo ◽

Dry Weight ◽

Sole Source ◽

Pha Synthase ◽

High Oleic ◽

Medium Chain Length ◽

Pha Production

Greater than 65% of canola and high-oleic soy oil fatty acids is oleic acid, which is readily converted to nonanoic (NA) and azelaic (AzA) acids by ozonolysis. NA is an excellent substrate for medium-chain-length polyhydroxyalkanoate (mcl-PHA) production but AzA has few uses. Pseudomonas citronellolis DSM 50332 and Pseudomonas fluorescens ATCC 17400, both able to produce mcl-PHA from fatty acids and to grow on AzA as the sole source of carbon and energy, were assessed for the accumulation of mcl-PHA from AzA and NA. In N-limited shake flasks using NA, P. citronellolis produced 32% of its dry biomass as mcl-PHA containing 78% 3-hydroxynonanoate with 22% 3-hydroxyheptanoate. Pseudomonas fluorescens produced only 2% PHA. N-limited P. citronellolis on AzA produced 20% dry weight PHA containing 75% 3-hydroxydecanoate and 25% 3-hydroxyoctanoate, indicative of de novo synthesis. Although selective pressure, including β-oxidation inhibition, under well-controlled (chemostat) conditions was applied to P. citronellolis, no side-chain carboxyl groups were detected. It was concluded that one or more of FabG and PhaJ or the PHA synthase cannot catalyze reactions involving ω-carboxy substrates. However, a process based on oleic acid could be established if Pseudomonas putida was engineered to grow on AzA.

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Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico

PeerJ ◽

10.7717/peerj.4780 ◽

2018 ◽

Vol 6 ◽

pp. e4780 ◽

Cited By ~ 5

Author(s):

Carolina A. Martínez-Gutiérrez ◽

Hever Latisnere-Barragán ◽

José Q. García-Maldonado ◽

Alejandro López-Cortés

Keyword(s):

Chain Length ◽

Microbial Mats ◽

Pha Synthase ◽

Rrna Gene ◽

Bacterial Strains ◽

Plastic Properties ◽

Medium Chain ◽

Medium Chain Length ◽

Pha Production ◽

Hypersaline Microbial Mats

Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to aHalomonassp. In addition,Paracoccussp.,Planomicrobiumsp. andStaphylococcussp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those ofPseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence ofphaCandphaC1sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.

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Fructose-Based Production of Short-Chain-Length and Medium-Chain-Length Polyhydroxyalkanoate Copolymer by Arctic Pseudomonas sp. B14-6

Polymers ◽

10.3390/polym13091398 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1398

Author(s):

Tae-Rim Choi ◽

Ye-Lim Park ◽

Hun-Suk Song ◽

Sun Mi Lee ◽

Sol Lee Park ◽

...

Keyword(s):

Molecular Weight ◽

Chain Length ◽

Average Molecular Weight ◽

Short Chain ◽

Pha Synthase ◽

Pseudomonas Sp ◽

Short Chain Length ◽

Medium Chain ◽

Medium Chain Length ◽

Pha Production

Arctic bacteria employ various mechanisms to survive harsh conditions, one of which is to accumulate carbon and energy inside the cell in the form of polyhydroxyalkanoate (PHA). Whole-genome sequencing of a new Arctic soil bacterium Pseudomonas sp. B14-6 revealed two PHA-production-related gene clusters containing four PHA synthase genes (phaC). Pseudomonas sp. B14-6 produced poly(6% 3-hydroxybutyrate-co-94% 3-hydroxyalkanoate) from various carbon sources, containing short-chain-length PHA (scl-PHA) and medium-chain-length PHA (mcl-PHA) composed of various monomers analyzed by GC-MS, such as 3-hydroxybutyrate, 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydecanoate, 3-hydroxydodecenoic acid, 3-hydroxydodecanoic acid, and 3-hydroxytetradecanoic acid. By optimizing the PHA production media, we achieved 34.6% PHA content using 5% fructose, and 23.7% PHA content using 5% fructose syrup. Differential scanning calorimetry of the scl-co-mcl PHA determined a glass transition temperature (Tg) of 15.3 °C, melting temperature of 112.8 °C, crystallization temperature of 86.8 °C, and 3.82% crystallinity. In addition, gel permeation chromatography revealed a number average molecular weight of 3.6 × 104, weight average molecular weight of 9.1 × 104, and polydispersity index value of 2.5. Overall, the novel Pseudomonas sp. B14-6 produced a polymer with high medium-chain-length content, low Tg, and low crystallinity, indicating its potential use in medical applications.

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Large scale function-based genome prospecting for industrial traits applied to 1,3-propanediol production.

10.1101/2021.08.25.457110 ◽

2021 ◽

Author(s):

Jasper J. Koehorst ◽

Nikolaos Strepis ◽

Sanne de Graaf ◽

Alfons J. M. Stams ◽

Diana Z. Sousa ◽

...

Keyword(s):

Large Scale ◽

Genome Mining ◽

Semantic Web Technologies ◽

Microbial Genomes ◽

The Public ◽

Web Technologies ◽

Candidate Species ◽

Important Trait ◽

Public Repositories ◽

Generation Sequencing

Due to the success of next-generation sequencing, there has been a vast build-up of microbial genomes in the public repositories. FAIR genome prospecting of this huge genomic potential for biotechnological benefiting, require new efficient and flexible methods. In this study, Semantic Web technologies are applied to develop a function-based genome mining approach that follows a knowledge and discovery in database (KDD) protocol. Focusing on the industrial important trait of 1,3-propanediol (1,3-PD) production 187 new candidate species were identified. Furthermore, the genetic architecture of the particular trait was resolved, and persistent domains identified.

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Polyhydroxyalkanoate (PHA) Production in Pseudomonas sp. phDV1 Strain Grown on Phenol as Carbon Sources

Microorganisms ◽

10.3390/microorganisms9081636 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1636

Author(s):

Iliana Kanavaki ◽

Athina Drakonaki ◽

Ermis Dionisios Geladas ◽

Apostolos Spyros ◽

Hao Xie ◽

...

Keyword(s):

Aromatic Compounds ◽

Carbon Sources ◽

Biodegradable Plastics ◽

Pha Synthase ◽

Pseudomonas Sp ◽

Degrading Bacterium ◽

Cell Extracts ◽

Transmission Electron ◽

Key Enzyme ◽

Pha Production

Pseudomonas strains have a variety of potential uses in bioremediation and biosynthesis of biodegradable plastics. Pseudomonas sp. strain phDV1, a Gram-negative phenol degrading bacterium, has been found to utilize monocyclic aromatic compounds as sole carbon source via the meta-cleavage pathway. The degradation of aromatic compounds comprises an important step in the removal of pollutants. The present study aimed to investigate the ability of the Pseudomonas sp. strain phDV1 to produce polyhydroxyalkanoates (PHAs) and examining the effect of phenol concentration on PHA production. The bacterium was cultivated in minimal medium supplemented with different concentrations of phenol ranging from 200–600 mg/L. The activity of the PHA synthase, the key enzyme which produces PHA, was monitored spectroscopically in cells extracts. Furthermore, the PHA synthase was identified by mass spectrometry in cell extracts analyzed by SDS-PAGE. Transmission electron micrographs revealed abundant electron-transparent intracellular granules. The isolated biopolymer was confirmed to be polyhydroxybutyrate (PHB) by FTIR, NMR and MALDI-TOF/TOF analyses. The ability of strain Pseudomonas sp. phDV1 to remove phenol and to produce PHB makes the strain a promising biocatalyst in bioremediation and biosynthesis of biodegradable plastics.

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Strategic deployment of riparian buffers and windbreaks in Europe can co-deliver biomass and environmental benefits

Communications Earth & Environment ◽

10.1038/s43247-021-00247-y ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Oskar Englund ◽

Pål Börjesson ◽

Blas Mola-Yudego ◽

Göran Berndes ◽

Ioannis Dimitriou ◽

...

Keyword(s):

Agricultural Production ◽

Large Scale ◽

Production Systems ◽

Riparian Buffers ◽

Environmental Benefits ◽

The European Union ◽

Negative Effects ◽

Nitrogen Emissions ◽

Environmental Objectives ◽

Eu Policies

AbstractWithin the scope of the new Common Agricultural Policy of the European Union, in coherence with other EU policies, new incentives are developed for farmers to deploy practices that are beneficial for climate, water, soil, air, and biodiversity. Such practices include establishment of multifunctional biomass production systems, designed to reduce environmental impacts while providing biomass for food, feed, bioenergy, and other biobased products. Here, we model three scenarios of large-scale deployment for two such systems, riparian buffers and windbreaks, across over 81,000 landscapes in Europe, and quantify the corresponding areas, biomass output, and environmental benefits. The results show that these systems can effectively reduce nitrogen emissions to water and soil loss by wind erosion, while simultaneously providing substantial environmental co-benefits, having limited negative effects on current agricultural production. This kind of beneficial land-use change using strategic perennialization is important for meeting environmental objectives while advancing towards a sustainable bioeconomy.

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Conservation of animal genetic resources: approaches and technologies for in situ and ex situ conservation

Animal Genetic Resources Information ◽

10.1017/s1014233900002571 ◽

2008 ◽

Vol 42 ◽

pp. 71-85 ◽

Cited By ~ 8

Author(s):

J.A. Woolliams ◽

O. Matika ◽

J. Pattison

Keyword(s):

Rural Communities ◽

Genetic Resources ◽

Large Scale ◽

Production Systems ◽

Regional Distribution ◽

Livestock Production ◽

Ex Situ ◽

Animal Genetic Resources ◽

The Face ◽

Livestock Products

SummaryLivestock production faces major challenges through the coincidence of major drivers of change, some with conflicting directions. These are:1. An unprecedented global change in demands for traditional livestock products such as meat, milk and eggs.2. Large changes in the demographic and regional distribution of these demands.3. The need to reduce poverty in rural communities by providing sustainable livelihoods.4. The possible emergence of new agricultural outputs such as bio-fuels making a significant impact upon traditional production systems.5. A growing awareness of the need to reduce the environmental impact of livestock production.6. The uncertainty in the scale and impact of climate change. This paper explores these challenges from a scientific perspective in the face of the large-scale and selective erosion of our animal genetic resources, and concludes thai there is a stronger and more urgent need than ever before to secure the livestock genetic resources available to humankind through a comprehensive global conservation programme.

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Within-Season Changes in Land-Use Impact Pest Abundance in Smallholder African Cassava Production Systems

Insects ◽

10.3390/insects12030269 ◽

2021 ◽

Vol 12 (3) ◽

pp. 269 ◽

Cited By ~ 1

Author(s):

Andrew Kalyebi ◽

Sarina Macfadyen ◽

Andrew Hulthen ◽

Patrick Ocitti ◽

Frances Jacomb ◽

...

Keyword(s):

Land Use ◽

Bemisia Tabaci ◽

Large Scale ◽

Production Systems ◽

Smallholder Farmers ◽

Negative Relationship ◽

Central Africa ◽

Sub Saharan Africa ◽

Smallholder Farming ◽

Manihot Esculenta Crantz

Cassava (Manihot esculenta Crantz), an important commercial and food security crop in East and Central Africa, continues to be adversely affected by the whitefly Bemisia tabaci. In Uganda, changes in smallholder farming landscapes due to crop rotations can impact pest populations but how these changes affect pest outbreak risk is unknown. We investigated how seasonal changes in land-use have affected B. tabaci population dynamics and its parasitoids. We used a large-scale field experiment to standardize the focal field in terms of cassava age and cultivar, then measured how Bemisia populations responded to surrounding land-use change. Bemisia tabaci Sub-Saharan Africa 1 (SSA1) was identified using molecular diagnostics as the most prevalent species and the same species was also found on surrounding soybean, groundnut, and sesame crops. We found that an increase in the area of cassava in the 3–7-month age range in the landscape resulted in an increase in the abundance of the B. tabaci SSA1 on cassava. There was a negative relationship between the extent of non-crop vegetation in the landscape and parasitism of nymphs suggesting that these parasitoids do not rely on resources in the non-crop patches. The highest abundance of B. tabaci SSA1 nymphs in cassava fields occurred at times when landscapes had large areas of weeds, low to moderate areas of maize, and low areas of banana. Our results can guide the development of land-use strategies that smallholder farmers can employ to manage these pests.

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Kinetics of medium-chain-length polyhydroxyalkanoate production by a novel isolate of Pseudomonas putida LS46

Canadian Journal of Microbiology ◽

10.1139/w2012-074 ◽

2012 ◽

Vol 58 (8) ◽

pp. 982-989 ◽

Cited By ~ 24

Author(s):

Parveen K. Sharma ◽

Jilagamazhi Fu ◽

Nazim Cicek ◽

Richard Sparling ◽

David B. Levin

Keyword(s):

Pseudomonas Putida ◽

Chain Length ◽

Saturated Fatty Acids ◽

Dry Mass ◽

Nucleotide Sequence Analysis ◽

Glucose Medium ◽

Medium Chain ◽

Medium Chain Length ◽

Pha Production ◽

Nitrogen Excess

Six bacteria that synthesize medium-chain-length polyhydroxyalkanoates (mcl-PHAs) were isolated from sewage sludge and hog barn wash and identified as strains of Pseudomonas and Comamonas by 16S rDNA gene sequencing. One isolate, Pseudomonas putida LS46, showed good PHA production (22% of cell dry mass) in glucose medium, and it was selected for further studies. While it is closely related to other P. putida strains (F1, KT2440, BIRD-1, GB-1, S16, and W619), P. putida LS46 was genetically distinct from these other strains on the basis of nucleotide sequence analysis of the cpn60 gene hypervariable region. PHA production was detected as early as 12 h in both nitrogen-limited and nitrogen-excess conditions. The increase in PHA production after 48 h was higher in nitrogen-limited cultures than in nitrogen-excess cultures. Pseudomonas putida LS46 produced mcl-PHAs when cultured with glucose, glycerol, or C6–C14 saturated fatty acids as carbon sources, and mcl-PHAs accounted for 56% of the cell dry mass when cells were batch cultured in medium containing 20 mmol/L octanoate. Although 3-hydroxydecanoate was the major mcl-PHA monomer (58.1–68.8 mol%) in P. putida LS46 cultured in glucose medium, 3-hydroxyoctanoate was the major monomer produced in octanoate medium (88 mol%).

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Identification and Characterization of a New Enoyl Coenzyme A Hydratase Involved in Biosynthesis of Medium-Chain-Length Polyhydroxyalkanoates in Recombinant Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.185.18.5391-5397.2003 ◽

2003 ◽

Vol 185 (18) ◽

pp. 5391-5397 ◽

Cited By ~ 64

Author(s):

Si Jae Park ◽

Sang Yup Lee

Keyword(s):

Escherichia Coli ◽

Fatty Acid ◽

Chain Length ◽

Biosynthetic Pathway ◽

Pha Synthase ◽

Enzymatic Analysis ◽

E Coli ◽

Medium Chain ◽

Medium Chain Length ◽

Enoyl Coa Hydratase

ABSTRACT The biosynthetic pathway of medium-chain-length (MCL) polyhydroxyalkanoates (PHAs) from fatty acids has been established in fadB mutant Escherichia coli strain by expressing the MCL-PHA synthase gene. However, the enzymes that are responsible for the generation of (R)-3-hydroxyacyl coenzyme A (R3HA-CoAs), the substrates for PHA synthase, have not been thoroughly elucidated. Escherichia coli MaoC, which is homologous to Pseudomonas aeruginosa (R)-specific enoyl-CoA hydratase (PhaJ1), was identified and found to be important for PHA biosynthesis in a fadB mutant E. coli strain. When the MCL-PHA synthase gene was introduced, the fadB maoC double-mutant E. coli WB108, which is a derivative of E. coli W3110, accumulated 43% less amount of MCL-PHA from fatty acid compared with the fadB mutant E. coli WB101. The PHA biosynthetic capacity could be restored by plasmid-based expression of the maoCEc gene in E. coli WB108. Also, E. coli W3110 possessing fully functional β-oxidation pathway could produce MCL-PHA from fatty acid by the coexpression of the maoCEc gene and the MCL-PHA synthase gene. For the enzymatic analysis, MaoC fused with His6-Tag at its C-terminal was expressed in E. coli and purified. Enzymatic analysis of tagged MaoC showed that MaoC has enoyl-CoA hydratase activity toward crotonyl-CoA. These results suggest that MaoC is a new enoyl-CoA hydratase involved in supplying (R)-3-hydroxyacyl-CoA from the β-oxidation pathway to PHA biosynthetic pathway in the fadB mutant E. coli strain.

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