Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen ...effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.
High-latitude fjords and continental shelves are shown to be sinks for atmospheric CO
2
, yet large spatial-temporal variability and poor regional coverage of sea-air CO
2
flux data, especially from ...fjord systems, makes it difficult to scale our knowledge on how they contribute to atmospheric carbon regulation. The magnitude and seasonal variability of atmosphere-sea CO
2
flux was investigated in high-latitude northern Norwegian coastal areas over 2018 and 2019, including four fjords and one coastal bay. The aim was to assess the physical and biogeochemical factors controlling CO
2
flux and partial pressure of CO
2
in surface water via correlation to physical oceanographic and biological measurements. The results show that the study region acts as an overall atmospheric CO
2
sink throughout the year, largely due to the strong undersaturation of CO
2
relative to atmospheric concentrations. Wind speed exerted the strongest influence on the instantaneous rate of sea-air CO
2
exchange, while exhibiting high variability. We concluded that the northernmost fjords (Altafjord and Porsangerfjord) showed stronger potential for instantaneous CO
2
uptake due to higher wind speeds. We also found that fixation of CO
2
was likely a significant factor controlling ΔpCO
2
from April to June, which followed phenology of spring phytoplankton blooms at each location. Decreased ΔpCO
2
and the resulting sea-air CO
2
flux was observed in autumn due to a combined reduction of the mixed layer with entrain of high CO
2
subsurface water, damped biological activity and higher surface water temperatures. This study provides the first measurements of atmospheric CO
2
flux in these fjord systems and therefore an important new baseline for gaining a better understanding on how the northern Norwegian coast and characteristic fjord systems participate in atmosphere carbon regulation.
Arctic marine environments are experiencing rapid changes due to the polar amplification of global warming. These changes impact the habitat of the cold-adapted microbial communities, which underpin ...biogeochemical cycles and marine food webs. We comparatively investigated the differences in prokaryotic and microeukaryotic taxa between summer surface water microbiomes sampled along a latitudinal transect from the ice-free southern Barents Sea and into the sea-ice-covered Nansen Basin to disentangle the dominating community (ecological) selection processes driving phylogenetic diversity. The community structure and richness of each site-specific microbiome were assessed in relation to the physical and biogeochemical conditions of the environment. A strong homogeneous deterministic selection process was inferred across the entire sampling transect
via
a phylogenetic null modeling approach. The microbial species richness and diversity were not negatively influenced by northward decreasing temperature and salinity. The results also suggest that regional phytoplankton blooms are a major prevalent factor in governing the bacterial community structure. This study supports the consideration that strong homogeneous selection is imposed across these cold-water marine environments uniformly, regardless of geographic assignments within either the Nansen Basin or the Barents Sea.
Systems biology: current status and challenges Zupanic, Anze; Bernstein, Hans C.; Heiland, Ines
Cellular and molecular life sciences : CMLS,
02/2020, Letnik:
77, Številka:
3
Journal Article
Recenzirano
Odprti dostop
We put together a special issue on current approaches in systems biology with a focus on mathematical modeling of metabolic networks. Mathematical models have increasingly been used to unravel ...molecular mechanisms of complex dynamic biological processes. We here provide a short introduction into the topics covered in this special issue, highlighting current developments and challenges.
► Ecological strategy, syntrophy, was built into artificial microbial consortia. ► Consortia comprised of engineered, byproduct-crossfeeding Escherichia. coli strains. ► Synthetic consortia ...demonstrated emergent property of enhanced biomass productivity. ► Consortia interactions produced predictable, self-assembling microlaminated biofilms. ► New synthetic biology strategy highlights potential biocatalyst platform technology.
Synthetic Escherichia coli consortia engineered for syntrophy demonstrated enhanced biomass productivity relative to monocultures. Binary consortia were designed to mimic a ubiquitous, naturally occurring ecological template of primary productivity supported by secondary consumption. The synthetic consortia replicated this evolution-proven strategy by combining a glucose positive E. coli strain, which served as the system's primary producer, with a glucose negative E. coli strain which consumed metabolic byproducts from the primary producer. The engineered consortia utilized strategic division of labor to simultaneously optimize multiple tasks enhancing overall culture performance. Consortial interactions resulted in the emergent property of enhanced system biomass productivity which was demonstrated with three distinct culturing systems: batch, chemostat and biofilm growth. Glucose-based biomass productivity increased by ∼15, 20 and 50% compared to appropriate monoculture controls for these three culturing systems, respectively. Interestingly, the consortial interactions also produced biofilms with predictable, self-assembling, laminated microstructures. This study establishes a metabolic engineering paradigm which can be easily adapted to existing E. coli based bioprocesses to improve productivity based on a robust ecological theme.
Microbial community succession is a fundamental process that affects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are often poorly ...understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the ecological contribution of colonizers? We performed a succession experiment within a hypersaline ecosystem to investigate how different processes contributed to the turnover of founder species. Bacterial and eukaryotic colonizers were identified during primary succession and tracked through a defined, 79-day biofilm maturation period using 16S and 18S rRNA gene sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate successional patterns of primary producers and nitrogen fixers. The majority of the founder species did not maintain high abundance throughout succession. Species replacement (versus loss) was the dominant process shaping community succession. We also asked if different ecological processes acted on bacteria versus Eukaryotes during succession and found deterministic and stochastic forces corresponded more with microeukaryote and bacterial colonization, respectively. Our results show that taxa and functions belonging to different kingdoms, which share habitat in the tight spatial confines of a biofilm, were influenced by different ecological processes and time scales of succession.
•A co-cultivation technology that converts, CH4 and CO2, into microbial biomass.•Robust bacterial growth on biogas and natural gas feedstocks.•Continuous co-cultivation without air or O2 feed to ...support CH4 oxidation.•A flexible co-culture technology constructed from genetically tractable bacteria.
A new co-cultivation technology is presented that converts greenhouse gasses, CH4 and CO2, into microbial biomass. The methanotrophic bacterium, Methylomicrobium alcaliphilum 20z, was coupled to a cyanobacterium, Synechococcus PCC 7002 via oxygenic photosynthesis. The system exhibited robust growth on diverse gas mixtures ranging from biogas to those representative of a natural gas feedstock. A continuous processes was developed on a synthetic natural gas feed that achieved steady-state by imposing coupled light and O2 limitations on the cyanobacterium and methanotroph, respectively. Continuous co-cultivation resulted in an O2 depleted reactor and does not require CH4/O2 mixtures to be fed into the system, thereby enhancing process safety considerations over traditional methanotroph mono-culture platforms. This co-culture technology is scalable with respect to its ability to utilize different gas streams and its biological components constructed from model bacteria that can be metabolically customized to produce a range of biofuels and bioproducts.
This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories ...central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.
Nannochloropsis gaditana is a promising microalga for biotechnology. One of the strategies to stimulate its full potential in metabolite production is exposure to flashing lights. Here, we report how ...N. gaditana adapts to different flashing light regimes (5, 50, and 500 Hz) by changing its cellular physiology and the relative expression of genes related to critical cellular functions. We analyzed the differential mRNA abundance of genes related to photosynthesis, nitrogen assimilation and biosynthesis of chlorophyll, carotenoids, lipids, fatty acids and starch. Analysis of photosynthetic efficiency and high mRNA abundance of photoprotection genes supported the inference that excess excitation energy provided by light absorbance during photosynthesis was produced under low frequency flashing lights and was dissipated by photopigments via the xanthophyll-cycle. Increased relative expression levels of genes related to the synthesis of carotenoids and chlorophyll confirmed the accumulation of photopigments previously observed at low frequency flashing lights. Higher differential mRNA abundance of genes related to the triacylglycerol biosynthesis were observed at lower frequency flashing lights, possibly triggered by a poor nitrogen assimilation caused by low mRNA abundance of a nitrate reductase gene. This study advances a new understanding of algal physiology and metabolism leading to improved cellular performance and metabolite production.
•Differential mRNA abundance was analyzed on N. gaditana exposed to flashing light (FL).•Excess energy dissipation via xanthophyll cycle was triggered at low frequencies FL.•High mRNA abundance of photopigment genes was promoted at low frequencies FL.•High mRNA abundance of Kennedy pathway genes observed at low frequencies FL.•Nitrate reductase transcripts showed low abundance at low frequencies FL causing nitrogen stress.
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