The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities

Cell Systems, Год журнала: 2024, Номер 15(1), С. 63 - 74.e5

Опубликована: Янв. 1, 2024

Язык: Английский

---

Revisiting the linkage between engineered ecosystem function and the microbial community: A review from ecological perspectives

Critical Reviews in Environmental Science and Technology, Год журнала: 2024, Номер 54(21), С. 1569 - 1591

Опубликована: Апрель 3, 2024

Biological waste treatment technology is currently the world's largest application process, and its functional achievement mainly relies on complex microbial communities. However, system in such engineered ecosystems has been considered a "black box." Over past decade, with development of molecular biotechnology next-generation sequencing technologies, exploration boxes" gradually deepened. In particular, role ecological forces uncovering regulating communities largely recognized provided novel insights into link between engineering objectives. study community ecology still early infancy faces grand challenges bridging principles theory. this review, we discuss recent advances understanding behavior biological systems, including biodiversity influencing factors, neglected rare species, interactions, assembly mechanisms. We emphasize importance these perspectives revealing functions, as enhancement contaminant removal operational stability ecosystems. cross-validation analysis results necessary to yield valid real information guide improvement ecosystem performance. Multi-omics approaches synthetic biology are preferred ways theory

Язык: Английский

---

Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater

Water Research, Год журнала: 2024, Номер 256, С. 121593 - 121593

Опубликована: Апрель 10, 2024

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic receiving water bodies, but knowledge molecular mechanisms driving contaminant biotransformations complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that experimental flume systems grown at higher ratios treated (WW) to displayed an increased biotransformation potential for number contaminants. We identified positive correlation between WW percentage and rates widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) other wastewater-borne with hydrolyzable moieties. Here, conducted deep shotgun sequencing metagenomic read abundances DEET hydrolase (DH) homologs. To test causality this association, constructed targeted library DH homologs biofilms. screened our complete activity four different substrates, DEET, subset thereof 183 WW-related compounds. The majority active hydrolases preferred aliphatic aromatic ester substrates while, remarkably, only single reference enzyme was capable hydrolysis. Of 626 total enzyme-substrate combinations tested, approximately 5% were pairs. Metagenomic family revealed broad substrate promiscuity spanning 22 compounds when summed across all enzymes tested. biochemically characterized most promiscuous based on analysis uncultivated Rhodospirillaceae Planctomycetaceae. In addition characterizing new enzymes, exemplified framework linking metagenome-guided hypothesis generation validation. Overall, study expands scope known enzymatic WW-receiving communities.

Язык: Английский

---

A new era of synthetic biology—microbial community design

Synthetic Biology, Год журнала: 2024, Номер 9(1)

Опубликована: Янв. 1, 2024

Abstract Synthetic biology conceptualizes biological complexity as a network of parts, devices, and systems with predetermined functionalities has had revolutionary impact on fundamental applied research. With the unprecedented ability to synthesize transfer any DNA RNA across organisms, scope synthetic is expanding being recreated in previously unimaginable ways. The field matured level where highly complex networks, such artificial communities can be constructed. In parallel, computational became an integral part studies, models aiding unravelling escalating emerging properties phenomena. However, there still vast untapped potential for complete integration modelling into design process, presenting exciting opportunities scientific advancements. Here, we first highlight most recent advances computer-aided microbial communities. Next, propose that benefit from organism-free modular approach places its emphasis modules organismal function towards multispecies We argue shift perspective single organism–centred approaches emphasizing functional contributions organisms within community. By assembling using mathematical descriptions parts circuits, tailor fulfil specific roles This aligns strategies presents possibilities Graphical

Язык: Английский

---

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

BMC Genomics, Год журнала: 2022, Номер 23(1)

Опубликована: Окт. 6, 2022

Abstract Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that mainly accumulated in oil reservoirs. As the introduction all classes hydrocarbons including crude products into environment has increased significantly, pollution become a global ecological problem. However, our perception pathways for biotic degradation major HCs key enzymes these bioconversion processes been based on cultured microbes is biased by uneven taxonomic representation. Here we used Annotree to provide gene-centric view aerobic ability aliphatic aromatic 23,446 genomes from 123 bacterial 14 archaeal phyla. Results Apart widespread genetic potential HC Proteobacteria, Actinobacteriota, Bacteroidota, Firmicutes, an additional 18 3 phyla also hosted degrading enzymes. Among these, such not previously reported representatives UBA8248, Tectomicrobia, SAR324, Eremiobacterota. Genomes containing whole complete were only detected Proteobacteria Actinobacteriota. Except several members Crenarchaeota, Halobacterota, Nanoarchaeota have tmoA, ladA, alkB/M genes, respectively, made small contribution degradation. None screened coded studied here; however, they contribute significantly peripheral routes with bacteria. Conclusion Phylogeny reconstruction showed reservoir hydrocarbon-degrading Bacteria Archaea undergoes extensive diversification via gene duplication horizontal transfer. This could potentially enable rapidly adapt novel manufactured reach environment.

Язык: Английский

---

Programming Dynamic Division of Labor Using Horizontal Gene Transfer

ACS Synthetic Biology, Год журнала: 2024, Номер 13(4), С. 1142 - 1151

Опубликована: Апрель 3, 2024

The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. introduction a complex, multistep pathway often imposes substantial burden on the host cell, restraining accumulation productive biomass limiting efficiency. One strategy to alleviate is division labor (DOL) in which different subpopulations carry out parts work together convert substrate into final product. However, maintenance engineered challenging due competition convoluted interstrain population dynamics. Through modeling, we show that dynamic (DDOL), define as DOL between indiscrete populations capable reversible interchange, can overcome these limitations enable robust burdensome, pathways. We propose DDOL be mediated by horizontal gene transfer (HGT) use plasmid genomics uncover evidence utilized natural microbial communities. Our suggests bioengineers harness HGT stabilize synthetic pathways communities, enabling development systems for deployment variety contexts.

Язык: Английский

---

Assembly of functional microbial ecosystems: from molecular circuits to communities

FEMS Microbiology Reviews, Год журнала: 2024, Номер 48(6)

Опубликована: Ноя. 1, 2024

Abstract Microbes compete and cooperate with each other via a variety of chemicals circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes bottom-up synthetic biology approaches for diverse applications. However, they separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, promising The strategies coordinating ecosystems based different regulation circuits not systematically summarized, which calls more comprehensive framework the assembly communities. In this review, we summarize cross-talk orthogonal modules de novo assembling functional ecosystems, thus promoting further consortia-based First, review communication-based regulations among various communities from intra-species inter-species aspects. Then, are summarized at metabolites, transcription, translation, post-translation levels, respectively. Furthermore, give details better design optimize propose design-build-test-learn procedure function specification, chassis selection, interaction design, system build, performance test, modeling analysis, global optimization. Finally, current challenges opportunities discussed development application ecosystems.

Язык: Английский

---

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

Plant Cell & Environment, Год журнала: 2025, Номер unknown

Опубликована: Янв. 2, 2025

How different stress responses by male and female plants are influenced interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant quantified biotic associations between microorganisms to explore the relationship microbial adaptation. We propose health index (HI) comprehensively characterize physiological characteristics adaptive capacity of under stress. It was found that poplars demonstrated higher salt tolerance than females, root-secreted citric acid significantly in rhizospheres poplars. Positive association among bacteria increased HI stress, while fungal cross-domain (bacteria-fungi) did not. further identified keystone bacterial taxon regulating association, ASV_22706, which itself regulated positively correlated host HI. The abundance taxa negatively Compared poplars, enriched more prebiotics probiotics This work primarily reveals adaptation differences plants, suggests approach improve adaptability conditions.

Язык: Английский

---

Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation

Biotechnology for Biofuels and Bioproducts, Год журнала: 2025, Номер 18(1)

Опубликована: Янв. 18, 2025

Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role lignin degradation coastal wetlands, where turnover rates likely underestimated. However, the metabolic potentials of these remain elusive. This greatly hinders our understanding global carbon cycle and "bottom-up" design synthetic to enhance conversion. Here, we developed two groups degrading consortia, L6 L18, through 6- 18-month situ enrichments East China Sea, respectively. Lignin by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon metagenomic sequencing suggested possessed varied taxonomic compositions, yet similar functional traits. Further comparative based on assembly, revealed harbored abundant metagenome-assembled genomes (MAGs) encoded diverse unique gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched highlighting degradation. Furthermore, generalist taxa, which possess flexibility, increased during extended enrichment period, indicating advantage generalists adapting heterogenous resources. study advances strategies prokaryotic lays foundation for communities sustainable lignocellulose biorefining.

Язык: Английский

---

Indigenous lignocellulose-degrading consortium efficiently degrade Traditional Chinese medicine residues

Industrial Crops and Products, Год журнала: 2025, Номер 226, С. 120641 - 120641

Опубликована: Фев. 6, 2025

---