Environmental Microbes Flashcards
earth’s upper atmosphere
remarkably harsh conditions - affect, if not control, climate.
certain environmental exposures could change quorum sensing
in a way that would present us with an impending health risk.
Rhizobia in symbiosis with nitrogen-fixing root nodules
takes part in producing iron-containing leghemoglobin.
White clover cryptic virus (WCCV)
prevents its host plants from forming a mutualistic association with Rhizobium bacteria if the soil contains enough nitrogen; saves the plant from wasting energy producing root nodules and donating sugar to the bacteria when it doesn’t need nitrogen.
Microbial Carbon Pump (MCP).
- photosynthetic microbes die; some of the carbon they fixed is released into the ocean as dissolved organic carbon - acts as a food source for non-photosynthetic marine microbes
- release some of the carbon back into the ocean as dissolved CO2 via respiration, some is recycled back to DOC when they are killed by viruses and the rest enters the marine food web when they are eaten by other marine organisms
- any DOC that is not consumed by marine microbes remains in the ocean carbon reservoir and slowly sediments to the ocean floor where it mineralizes to form rock: a carbon sink that lasts for millions of years.
heat-stable Taq polymerase from Thermus aquaticus
enabled the development of PCR
restriction endonucleases that bacteria produce to defend themselves against bacteriophages
are very useful in cloning because they cut DNA at specific sequences
soil warming experiment effect on
heat shock and cold shock proteins
adaptive responses
dormancy, carbon storage and osmolyte reservation and extracellular polymeric substance production
stresses
e.g. osmotic and drought
organic matter inputs
such as phytohormones
applying plant growth-promoters to seed coatings
such as Rhizobium for nitrogen fixation, IAA for root production and N2O-consuming communities ammonia oxidation pathway inhibitors
endophytes as phyllospheric inoculants
specifically for phosphate solubilization, in legumes
CLSM and integration green fluorescent protein cassette biomarking and nif overexpression
may allow the development of similar associations in non-leguminous plants,
changes in soil organic carbon availability and aridity (caused by desertification) in cryptogamic soil
with relevance to bacterial and fungal concentration, to determine drought-sensitivity and the differential changes in the bulk microbiome and plant community dispersal structure (e.g. C4 or C3 plants) that will occur, and how inter-kingdom interactions can be harnessed to connect resource islands
land degradation, erosion, increased solar penetration, albedo alterations, pH shifts and organic layer soil combustion on species with differing natural fire resiliences
to avoid the pasteurization that would destroy soil aggregate structure, reducing aeration and result in proliferation of pathogenic taxa, and a degraded ecosystem
resource depletion due to
reduced snowpack, increasing freeze-thaw cycles and salt-intrusion on methanogenesis, denitrification and redox cycling dynamics
transition of peatlands from carbon sinks to sources
and to prevent boom and bust
Managing carbon and photosynthate rhizodeposition (and litter) input (through root exudation and sloughed root cap cells)
through autotrophic sequestration and other biochemical transformation pathways for bioavailable microbial exchange in the soil matrix and persistence in recalcitrant end products will have greater efficacy if biodiversity is maintained
arbuscular mycorrhizal fungi
for regulation of aquaporins
plant genetic modification
for selection of root- colonizing symbioses to optimise the plant-microorganism-soil system
identification of rhizospheric endo- and ectosymbioses…
… such as syntrophy
panomic attempts to overcome the difficulties presented by
microbe-physiology heterogeneity and electron acceptor availability, spatiotemporal variability, the highly structured and yet dynamic environment and relic DNA obscurities.
New technological advances
sensitive mass spectrometry, long-read sequencing technologies, high-throughput sequencing studies, deep metagenome sequencing, computational approaches, fluxomics, gap filling, microfluidics and stable isotope probing, could be utilised at the micro-relevant scale
isolation and functional gene annotation of microbes, identification of dominant heterotrophic pathways and elucidating metabolic interdependencies and cooperation at a community level
through bioprospecting microbial network metabolism and complementary metabolic output
the transition from metagenome to metaphenome involves
establishing soil community genes, and refining chains of expression through the metatranscriptome and metaproteome data, will allow the construction of a naturally evolved and tractable model soil consortia in the soil environment, allowing the study of metabolic and spatial interactions through chemical signalling
combining soil isolates into synthetic communities
to organise complex microbiomes into guilds should allow the creation of genome bins to allow the application of comparative genomics, which will all be imperative in the understanding of microbial response to perturbation
