1. INTRODUCTION:
CARBON:-
“Besides water, one of the most important requirements for microbial growth is carbon.
Carbon is the structural backbone c of living matter, it is needed for all the organic compounds
that make up a living cell. Half the dry weight of a typical bacterial cell is carbon. Chemo
heterotrophs get most of their carbon from the source of their energy-organic materials such as
proteins, carbohydrates, and lipids. Chemoautotrophs and photo autotrophs derive their carbon
from carbon dioxide.” Willey ,Sherwood 7th edition
SOURCE OF CARBON
HETEROTROPH:-
“A heterotroph must use one or more organic compounds as its source of carbon.”
Organic compounds:-
• Protein
• Carbohydrate
• Lipids
AUTOTROPH:-
“An autotroph can derive its carbon from carbon dioxide.”
• Carbon Dioxide
REQUIREMENTOF CARBON:-
“All organisms need carbon and its derivatives. Carbon is needed to synthesize the
organic molecules from which organisms are built. The requirements for carbon, hydrogen, and
electron usually are satisfied together because molecules serving as carbon sources often
contribute hydrogen as well. For instance, many heterotrophs-organisms that use reduced,
preformed organic molecules as their carbon source can also obtain hydrogen, oxygen, and
electrons from the same molecules. Because the electrons provided by these organic carbon
sources can be used in electron transport as well as in other oxidation-reduction reactions, many
heterotrophs also use their carbon source as an energy source. Indeed, the more reduced the
organic carbon source (i.e., the more electrons it carries), the higher its energy. Thus lipids have
a higher energy content than carbohydrates. Carbohydrates, Lipids.”
Tortora, Funke,Case(12th Edition)
2. HETEROTROPHS:-
“A most remarkable characteristic of heterotrophic microorganisms is their
extraordinary flexibility with respect to carbon sources. Laboratory experiments indicate that
all naturally occurring organic molecules can be used as a source of carbon or energy or both
by at least some microorganisms Actinomycetes, common soil bacteria, degrade amyl alcohol,
paraffin, and even rubber. The bacterium Burkholderia cepacia can use over 100 different
carbon compounds. Microbes can degrade even relatively indigestible human-made substances
such as pesticides. This is usually accomplished in complex microbial communities. These
molecules sometimes are degraded in the presence of a growth-promoting nutrient that is
metabolized time-a process called cometabolism. Other microorganisms can use the products
of this breakdown process as nutrients. In contrast to these bacterial omnivores, some microbes
are exceedingly fastidious and catabolize only a few carbon compounds. Cultures of
methylotrophic bacteria microbes’ methane, methanol, carbon monoxide, formic acid, and
related carbon molecules. Parasitic members of the genus Leptospira use only long-chain fatty
acids as their major source of carbon and energy. Biodegradation and bioremediation by natural
Communities.” . M. Willey,M. Sherwood(8th Edition
Heterotrophic microbial activity and organic matter degradation:-
“Whereas zooplankton requires particulate organic material as a food source, the heterotrophic
bacteria are the only important group of organisms (concerning their role in carbon dynamics) that can
use particulate as well as dissolved organic matter. The bacteria, therefore, play a key role in the cycling
of organic carbon in aquatic environments (William 1981). The total decomposition of particulate and
dissolved organic substances can easily be determined by measuring the community respiration. This
is one of the simplest and least ambiguous estimations of heterotrophic metabolic activity that can be
directly related to organic matter oxidation (Biddanda, B., S. Opsahl & R. Benner. 1994). On the other hand, the
direct determination of bacterial respiration is a difficult task. Although microbial respiration rates are
higher per unit biomass than those of larger organisms, the respiration rate per unit volume of water
(especially in low productive systems) is often too small to be measured directly. In productive coastal
environments, however, a fractionated filtration (i.e. the separation of bacteria from other organisms
using filters of small pore size), preceding respiration measurements, might be a way to achieve this
goal, but a clear separation is mostly impossible due to size overlapping of bacteria with the smallest
algae and nanoflagellates. The contribution of bacteria to community respiration, therefore, has to be
determined in an indirect form which can be done by first determining bacterial secondary production
and then calculating bacterial respiration by assuming a certain growth efficiency. There are, however,
several uncertainties. First, the determination of bacterial secondary production from incorporation rates
of tritiated thymidine or leucine requires the adoption of several conversion factors. Then a specified
factor for growth efficiency has to be used. None of these factors is stable as each varies according to
3. environmental conditions. Taking all these problems together, the determination of bacterial respiration
remains a complicated problem.”
REQUIREMENTOF ORGANIC MATERIAL:-
1. Mechanisms for Induction of MicrobialExtracellularProteasesin
Response to Exterior Proteins:-
“Proteins are the main organic nitrogen source for microorganisms. Many heterotrophic
microorganisms secrete extracellular proteases (ex-proteases) to efficiently decompose
proteins into oligopeptides and amino acids when exterior proteins are required for growth.
These ex-proteases not only play important roles in microbial nutrient acquisition or host
infection but also contribute greatly to the global recycling of carbon and nitrogen. Moreover,
may microbial ex-proteases have important applications in industrial, medical, and
biotechnological areas. Therefore, uncovering the mechanisms by which microorganisms
initiate the expression of ex-protease genes in response to exterior proteins is of great
significance. In this review, the progress made in understanding the induction mechanisms of
microbial ex-proteases in response to exterior proteins is summarized, with a focus on the
inducer molecules, membrane sensors, and downstream pathways. Problems to be solved for a
better understanding of the induction mechanisms of microbial ex-proteases are also
discussed.” Chen XL, Zhang YZ, Gao PJ, Luan XW. 2003
2. Requirement Of Lipid In Microbial Growth:-
“Results concerning the ruminal fluid growth requirement of the ruminal
acetogen, Syntrophococcus sucromutans, indicate that octadecenoic acid isomers
satisfy this essential requirement. Complex lipids, such as triglycerides and
phospholipids, can also support growth. The cellular fatty acid and aldehyde
composition closelyreflects that ofthe lipid supplement providedto the cells. Up to 98%
of the fatty acids and 80% of the fatty aldehydes are identical in chain length and degree
of unsaturation to the octadecenoic acid supplement provided in the medium. S.
sucromutans shows a tendency to have a greater proportion of the aldehyde form
among its 18 carbon chains than it does with the shorter-chain simple lipids, which may
be interpreted as a strategy to maintain membrane fluidity. 14C labeling showed that
most of the oleic acid taken up from the medium was incorporated into the membrane
fraction of the cells.” BLIGH EG, DYER WJ. 1959
4. Synthetic Microbial Communities Of Heterotrophs And Phototrophs
Facilitate Sustainable Growth
“Phototrophic microbial communities exhibit symbiosis between
photoautotrophic and heterotrophic organisms supported primarily by solar energy
and the fixation of carbon dioxide (CO2). This type of association dominates many
biofilms, microbial mats, and lichens Stuart, R. K. et al. 2016, thriving in desiccation, nutrient
starvation, and salinity or temperature extremes. This ability to survive extreme
conditions is due, in part, to the division of labor and subsequent interactions between
members of the community. Photoautotrophic members, classically either
cyanobacteria or eukaryotic algae, convert CO2 into organic carbon for growth and
maintenance of the heterotrophic partner(s). The exchange of these metabolites can
sustain the heterotrophs under conditions devoid of any organic carbon source. In
turn, the heterotrophs provide additional CO2, protection from environmental factors
and predation, and often, a diverse array of metabolites produced by secondary
Metabolism” Makkonen, S., Hurri, R. S. K. & Hyvarinen877-884
“To date, understanding, engineering, and determining viable cultivation conditions
for natural phototrophic communities remains challenging. Thus, synthetic
communities have been the primary platform for autotrophic-heterotrophic
symbioses for bioenergy, resulting in novel phototrophic systems to produce biomass
and value-added compounds. Synthetic phototrophic communities (SPCs) have been
utilized for the production of biofuels, α-amylase, and polyhydroxyalkanoates
among other compounds. Complex communities consisting of algae and bacteria
also have potential applications in waste-water treatment, bioremediation, and as a
bloom control method for phytoplankton. Traditionally, microbial communities have
been selected in long term adaptation and optimization experiments to define optimal
culture conditions. The critical challenge in synthetic community design is to
maintain syntrophic interactions between members to avoid culture collapse..”
5. BIOPRODUCTIONON
“Development of SPCs for bioproduction involves four critical steps: (a)
strain selection, (b) screening of cultivation conditions, (c) efficient extraction of
addedvalue products, and (d) process control and biomass recycling. The first three
steps (a–c) are important drivers for the implementation of successful bioproduction
processes that can be optimized and guided using metabolic modeling.”
“Constraint-based metabolic modeling is a systems biology tool that provides a comprehensive
metabolic understanding about individual microorganisms (metabolic models henceforth
referred to as M-models and microbial communities (community-metabolic models henceforth
referd to as CM-models). These models account for biochemical and genomic information for
an individual or community at the genome-scale. Resulting models are solved using flux
balance analysis and can accurately predict thousands of functional states. Simulations
performed with CM-models describe key metabolic functions of microbial communities,
defining all possible interactions among partners based on genetic and/or metabolic fitness.
CM-models also enable prediction of effective culture conditions for production in robust
biotechnological processes. “
Autotrophs
“Other microbes are autotrophs-organisms that use carbon dioxide (CO2) as their sole
or principal source of carbon. Although CO2 is plentiful, its use as a carbon source presents a
problem to autotrophs. CO2 is the most oxidized form of carbon, lacks hydrogen, and is unable
to donate electrons during oxidation-reduction reactions. Therefore CO2 cannot be used as a
source of hydrogen, electrons, or energy. Because CO₂ cannot supply their energy needs,
autotrophs must obtain energy from other sources, molecules.”
“Phototrophs use light as their energy source: chemotropism obtain energy from the oxidation
of chemical compounds (either organic or inorganic). Microorganisms also have only two
sources for electrons. Lithotrophs (i.e., "rock-eaters") use reduced inorganic substances as their
electron source, whereas organography extract electrons from reduced organic compounds.”
Tortora. Funke,Case(Tenth Edition)
A Review of Effects of Carbon Dioxide on Microbial Growth:-
“Carbon dioxide is effective for extending the shelf-life of perishable foods by
retarding bacterial growth. The overall effect of carbon dioxide is to increase both the lag phase
and the generation time of spoilage microorganisms; however, the specific mechanism for the
6. bacteriostatic effect is not known. Displacement of oxygen and intracellular acidification were
possible mechanisms that were proposed, then discounted, by early researchers. Rapid cellular
penetration and alteration of cell permeability characteristics have also been reported, but their
relation to the overall mechanism is not clear. Several researchers have proposed that carbon
dioxide may first be solubilized into the liquid phase of the treated tissue to form carbonic acid
(H2C03), and investigations by the authors tend to confirm this step to indicate the possible
direct use of carbonic acid for retarding bacterial spoilage. Most recently, a metabolic
mechanism has been studied by a number of researchers various carbon dioxide in the cell has
negative effects on various enzymatic and biochemical pathways. The combined effects these
metabolic interferences are thought to constitute a stress on the system, and result in a slowing
of the growth rate. The degree to which carbon dioxide is effective generally increases with
concentration, but high levels raise the possibility of establishing conditions where pathogenic
organisms such as Clostridiumbotulinummay survive. It is thought that such risks can be mini
control proper sanitation and temperature control and that the commercial development of food
packaging systems employing carbon dioxide will increase in the coming years.”
Stuart, R. K. et al 1240–1251
Requirement of CO2 for microbial Growth:
“It has been known for a long time that some bacteria require an atmosphere with high
CO2 levels for their growth. In 1952, Tuttle and Scherp reported that Neisseria
meningitides grew effectively under an atmosphere containing 4% CO2. Since then, the
dependence of a number of pathogens and ruminal bacteria on an atmosphere with high
levels of CO2 has been demonstrated; these microorganisms are called “capnophiles.”
Recently, several instances of a high-CO2 requirement with regard to the commensal
growth of some bacteria have been reported. For example, Diaz et al. reported that the
growth of Porphyromonas gingivalis depends on CO2 supplied by coexisting
Fusobacterium nucleatum. Bringel and Hubert revealed the presence of a number of CO2-
dependent auxotrophs in a community of lactic acid bacteria. Recently, we revealed that
Symbiobacterium thermophilum, a taxonomically unique syntrophic bacterium whose
growth depends on coculture with cognate Geobacillus stearothermophilus strain
demonstrated marked pure growth when CO2 was introduced into the culture”. Marín, D. et
al. 354–358 (2018).
“Despite such wide occurrence of capnophilic bacteria, CO2 is not conventionally supplied
to cultures used to isolate microorganisms from environmental samples. This made us
7. speculate that some microorganisms dependent on high CO2 levels have not yet been
isolated and that they remain uncharacterized despite their culturability. Hence, we
screened for bacteria whose isolation depended on the presence of an atmosphere with
high levels of CO2 by focusing on soil and water samples and studied the phylogenetic
affiliations of these bacteria.” Marín, D. et al.354–358 (2018).
“Prior to isolation, the effect of an atmosphere with high levels of CO2 on the colony
formationefficiency ofbacteria fromenvironmental samples was studied by microcolony
counting. An appropriately diluted environmental sample was applied to a 0.45-μm
nitrocellulose membrane disk (F4 cm; Advantec, Tokyo, Japan), which was divided into
two pieces. The pieces were placed separately on two Luria-Bertani (LB)
mediumcontaining agar plates containing tryptone (Difco Laboratories, Detroit, MI; 10
g/liter), yeast extract (Difco; 5 g/liter), NaCl (Kokusan, Tokyo, Japan; 5 g/liter), and agar
(Kokusan; 10 g/liter). The pH of the medium was adjusted to 7.0 and 9.0 for neutral and
alkaline samples using 50 mM phosphate and bicarbonate buffer, respectively. One plate
was incubated underambient air, and the otherwas incubated underan atmospherewith
high levels of CO2 (air supplied with 5% CO2) using a CO2 incubator (model 5400; Napco,
OH). After an 8-h incubation at 28°C, a filter was stained with methylene blue, and the
microcolony content was determined by direct counting under a stereo microscope. “
Zuñiga, C. et al. 123, 285–295(2015).
“Further, the effect of the atmosphere with high levels of CO2 on the diversity of the
bacteria grown from environmental samples was roughly estimated by denaturing
gradient gel electrophoresis (DGGE) analysis. Similar to the procedures described above,
the soil and water samples (neutral/alkaline) were inoculated into LB liquid medium (pH
7.0 or 9.0) and cultured at 28°C for 8 h. Then, the microbial cells were harvested by
centrifugation and subjected to DNA extraction. The resulting DNA fraction containing
the genomes of various bacteria was analyzed by DGGE using primers that extensively
amplified the bacterial 16S rRNA gene. The methods used for DNA extraction and DGGE
analysis have been described previously. The obtained DGGE profiles showed a marked
difference in the populations of cultures cultivated under 5% CO2 and those cultivated
under ambient air (for examples, see Fig. S1 in the supplemental material), suggesting
that the atmospheric CO2 content affects not only the number but also the diversity of the
bacteria that grow from environmental samples.” Hays, S. G. & Ducat, D. C. 123, 28
