Nutrient Use and Remineralization

Walter K. Dodds , in Freshwater Ecology, 2002

STOICHIOMETRY OF HETEROTROPHS, THEIR Nutrient, AND Food REMINERALIZATION

Heterotrophs remineralize nutrients when they are in backlog of requirements. The stoichiometry of many heterotrophs is similar to that of the Redfield ratio, and they are generally much less flexible than primary producers at altering these ratios. Because heterotrophic organisms need to meet both their energy and carbon demands for growth from the organic material they swallow, the nutrients in the nutrient they eat can frequently exceed the amount needed.

As an instance of the stoichiometric effects of the carbon requirement for both growth and respiration, consider a fish that is able to convert only x% of the carbon information technology consumes into biomass. The remaining 90% of the carbon must be used to create energy for metabolism. If food is consumed that has the Redfield ratio of 106:16:i mol of C:Northward:P, only 1/10th of the C, N, and P can be used for growth. The excess North and P will be excreted.

Food for heterotrophs is not always at the Redfield ratio, and requirements of all heterotrophs are not the same as the Redfield ratio. Consideration of stoichiometry has led to much written report of the requirements for ratios of nutrients, the stoichiometry of heterotrophs, and the limerick of their food.

Well-nigh bacterial heterotrophs rely on dissolved organic material for carbon, nitrogen, and phosphorus requirements. This material ultimately comes from primary producers (either phytoplankton in lakes or benthic algae and terrestrial vegetation in wetlands and streams) and can vary considerably in stoichiometry, every bit discussed previously. Bacteria tin can retain Northward increasingly equally the C:N ratio of the dissolved, organic material consumed decreases; thus, cyberspace remineralization is high at low C:Northward ratios (Fig. xvi.x).

FIGURE 16.10. Nitrogen retention efficiency as a office of C:N ratio of nutrient source for bacteria. Note that when food is relatively North rich (i.e., C:Due north is low), a low percentage of the N is utilized and most of the Due north ingested is remineralized

 (redrawn from Goldman et al., 1987). Copyright © 1987

The dissolved organic carbon bachelor to leaner may be poor in N and P, and they may need to run across their requirements for these materials by incorporating (also referred to as immobilizing or assimilating) inorganic forms, such as nitrate, ammonium, and phosphate (Tezuka, 1990). Thus, a significant portion of inorganic nutrient uptake in some lakes can be attributed to bacteria (Currie and Kalff, 1984; Dodds et al., 1991).

Ecosystem processes (eastward.thousand., remineralization) can exist tied to stoichiometry of organisms (Elser et al., 1996). For example, copepods have a higher N:P ratio than the cladoceran Daphnia (Fig. xvi.11). The low Northward:P ratio of Daphnia means that it has a relatively high P requirement for growth (Sterner, 1993). This requirement can atomic number 82 ultimately to more intense P limitation in lakes (Elser and Hassett, 1994). The high requirement of Daphnia for P can lead to a shift to stronger P limitation in phytoplankton (Sterner, 1990; Sterner et al., 1992) because of preferential assimilation of P relative to N and relatively high ratios of Northward:P in nutrients remineralized by Daphnia (Sterner and Hessen, 1994). Thus, the concepts of stoichiometry and nutrient limitation have implications for food webs and ecosystem role.

Figure sixteen.11. Data showing N:P ratio of Daphnia is lower than that of copepods, indicating different food requirements for both types of grazers

 (reproduced with permission from Elser et al., 1996. © American Institute of Biological Science). Copyright © 1996

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Enzymes and Nitrogen Cycling

John A. Berges , Margaret R. Mulholland , in Nitrogen in the Marine Surround (Second Edition), 2008

2.3.3.one Overview

Heterotrophs represent a major sink for primary product, and thus a disquisitional function of the marine N cycle. In the pelagic realm, in that location have been attempts to guess zooplankton grazing (both micro- and macro-zooplankton) using two major enzymatic approaches: activities of digestive enzymes (peculiarly proteases in the case of N) (east.thousand., Gonzalez et al., 1993) and the activity of GDH, the cardinal step in the pathway of excretion of NH4 + following catabolism of protein (e.g., Bidigare et al., 1982; Mayzaud, 1987; Park et al., 1986). Attention has as well been given to the digestive enzymes of benthic heterotrophs, though this has been related more than to assessing digestive acclimation and food quality than to quantifying rates. Digestive enzymes have been examined in connection with food supply and feeding rates (eastward.g., Mayer et al., 1997), and to aid make up one's mind what materials might exist degraded by unlike species in unlike environments (Roberts et al., 2001).

Figure 32.iii. Turnover time for the fluorescent compound LYA-tetra-alanine by cultures of different phytoplankton species and taxa

 (data from Mulholland and Lee, in revision).

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Future directions in photosynthetic organisms-catalyzed reactions

Kaoru Nakamura , in Hereafter Directions in Biocatalysis, 2007

one INTRODUCTION

Heterotrophs such every bit fungus, bacteria, and yeasts have been used as biocatalysts for biotransformation of organic compounds to afford useful compounds such as chiral intermediates for medicines. On the reverse, autotrophs such equally establish cell and microalgae are rare to be utilized for biotransformations, and investigation is necessary because they are environment-friendly catalysts: they blot carbon dioxide to generate oxygen using solar energy. Amidst photosynthetic organisms, microalgae are expected to class a new grouping of biocatalysts because of the high growth rates compared to plant cells. In this chapter, reduction, oxidation, and hydroxylation using algae are introduced. Ecology remediation using algae is also explained.

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Trophic Dynamics and Food Webs in Aquatic Ecosystems☆

U. Gaedke , in Reference Module in Earth Systems and Environmental Sciences, 2021

Food quality and quantity

Heterotrophs (consumers, including leaner) live by consumption of biomass or nonliving organic thing. Due to the chemical limerick of biomass (disregarding skeletal material or support structures) beyond all heterotrophs falls within a relatively narrow range, carnivores that feed on other heterotrophs are assimilating approximately the aforementioned mixture of elements that they volition need in order to synthesize their own biomass (skeletal fabric and support structure typically pass through the gut unassimilated). Hence, their food quality is high. Detritivores also do good from this carryover of elemental mixtures from one kind of organism to another, although detritus is more likely to show some selective loss of elements such every bit nutrients that would alter the balance typical of living biomass.

Unlike heterotrophs, photoautotrophs assimilate elements separately from h2o or, if they are rooted vascular plants, from sediments. For example, carbon is derived from H2CO3 and related inorganic carbon forms dissolved in h2o, and phosphorus is taken up separately equally phosphoric acid that is dissolved in h2o. Large imbalances may develop when some essential components are much more abundant than others because the inorganic substances required to synthesize biomass are taken up separately. For example, phytoplankton has a high carbon:food ratio under nutrient-depleted conditions. Thus, autotrophs face greater challenges than carnivores in assembling the necessary ratios of elements to synthesize biomass, but as well herbivores (and bacteria) can feel imbalances of elements.

The approximate ratios of elements that are characteristic of autotrophic biomass have been extensively studied. Feature ratios of carbon to nitrogen and phosphorus are ofttimes the greatest focus of assay. Considering carbon is the feedstock for photosynthesis and phosphorus and nitrogen are the two additional elements that are often in short supply for conversion of photosynthetic products (carbohydrates) to other molecule types that are needed for the synthesis of protoplasm (e.g., amino acids which are rich in Due north, or RNA which is rich in P). The importance of C:Northward:P ratios in aquatic organisms was first brought out by Alfred Redfield (1890–1983), who discovered that healthy oceanic phytoplankton show a characteristic molar C:N:P ratio of almost 106:16:one. Thus, the nutrient status of a phytoplankton community can be judged to some caste from the elemental ratios. For example, a phytoplankton customs suffering phosphorus deficiency may show a C:P ratio of 500:one rather than 106:1, as predicted by the Redfield Ratio for well-nourished phytoplankton. The assay of elemental ratios for diagnosis of elemental imbalances is termed "ecological stoichiometry" (Sterner and Elser, 2002).

Imbalances in elemental ratios in i trophic level tin can create imbalances in the diet and thus an inefficient transfer of energy to the side by side trophic level. This is particularly true between primary producers and herbivores. For example, plants suffering phosphorus scarcity may laissez passer biomass with a high C:P ratio to their grazers. The grazers must and then consume extra food in club to obtain the correct rest for the synthesis of their own biomass because of an imbalance of elements in the nutrient. Similarly, an especially low C:P ratio (e.1000., 50:1) will provide an crowd of phosphorus (due east.g., when bacteria are consumed), a large part of which is released to the surroundings without generating any biomass.

Another strategy that herbivores may employ in improving the elemental balance of food intake is to consume heterotrophs in addition to autotrophs (omnivory, which is feeding at multiple trophic levels) every bit animals and leaner are generally more nutrient rich than autotrophs. Thus, combining the consumption of a phosphorus-rich nutrient (high quality) with a carbon-rich food (often bachelor in high quantity, eastward.g., grass), enables a more efficient utilize of ingested mass than a single food blazon.

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Phytoremediation

S.C. McCutcheon , South.E. Jørgensen , in Encyclopedia of Ecology, 2008

Phytoremediation and Other Biotechnologies

'Phytoremediation' is the cleanup or control of wastes, specially hazardous wastes, using greenish plants. There are many types of phytoremediation, as shown in Table i , including the utilize of phreatophytes to control plumes of groundwater contaminants and contaminated vadose zones. Photoautotrophs, including vascular plants, dark-green algae, cyanobacteria, and fungi, must be involved in the synthesis or maintenance of biomass, or in the direct metabolism, storage, detoxification, or control of contaminants. Glycosylation, occurring in plants and saprophytic fungi but not bacteria, is commonly important in direct metabolism, detoxification, and accumulation or storage of pollutants by plants. Glycosylation is a sequestration of contaminant molecules by the improver of a glycosyl grouping to form a glycoprotein that found cells tin easily transport and store or transform. Not all applications of phytoremediation involve glycoproteins simply the occurrence of glycosylation in pollutant transformations does distinguish whether the metabolism of organic contaminants or transformation of other contaminants is bioremediation or phytoremediation.

Table 1. Types of phytoremediation ranked in terms of sustainability and applicability

Type Definition Applications
Phytodegradation: phytoassimilation, phytotransformation, phytoreduction, phytooxidation, and phytolignification Aquatic and terrestrial plants accept upwardly, store, and biochemically degrade or transform organic compounds to harmless by-products, products used to create new establish biomass, or by-products that are farther broken down by microbes and other processes to less harmful compounds. Growth and senescence enzymes, sometimes in serial, are involved in plant metabolism or detoxification. Reductive and oxidative enzymes may be serially involved in different parts of the establish Soils, sediments, wetlands, wastewaters, surface waters, groundwater, and air contaminated with chlorinated solvents (CCl4, trichloromethane, tetrachloromethane, HCA, PCE, TCE, DCE, and VC), methyl bromide, tetrabromoethene, tetrachloroethane, dichloroethene, atrazine, DDT, other Cl- and P-based pesticides, PCBs, phenols, anilines, nitriles, TNT, DNT, RDX, HMX, NB, picric acid, NT, nitromethane, nitroethane, and nutrients. Field sit-in: Iowa Regular army Ammunition Plant successfully restored using wetland plants (TNT and RDX). Proof of principle: (a) field – Populus spp. Carswell Air Force Base, Texas; Aberdeen Proving Grounds, Maryland; and using lysimeters at Tacoma, Washington (TCE); and (b) horseradish peroxidase pilot-tested in unit of measurement process to degrade phenols, aniline, and other aromatic contaminants in wastewater. Proof of concept: Rosa spp. cv. Paul'due south Scarlet (PCBs).
Phytostimulation: rhizodegradation, rhizosphere bioremediation, and establish-assisted bioremediation Constitute exudation, root necrosis, and other processes provide organic carbon and nutrients to spur soil leaner growth by 2 or more orders of magnitude in number; stimulate enzyme consecration and cometabolic degradation by mycorrhizal fungi and the rhizomicrobial consortium; provide various root zone habitat; and attenuate chemical movements and concentrations. Live roots transfer oxygen to aerobes, and dead roots may support anaerobes or go out aeration channels Soils and wetlands contaminated with crude oil, BTEX, other petroleum hydrocarbons, PAHs, PCP, perchlorate, pesticides, PCBs, and other organic compounds. Field proof of concept: BTEX, other hydrocarbons, PAHs, PCP, and TCE. Field tests: crude oil in wetlands of Spartina alterniflora and S. patens. Fungi: (i) field-scale tests: of white rot fungus degradation of BTEX and (2) proof of concept: for DDT, dieldrin, endosulfan, pentachloronitrobenzene, and PCP.
Phytocontainment: Trees and other phreatophytes transpire large quantities to contain shallow groundwater plumes or contaminated soil leaching by reversing horizontal aquifer hydraulic gradients, or vertical soil moisture force per unit area gradients (infiltration and leaching minimized) both year-round or seasonally to fully or partially capture contaminants. Applications normally coupled with rhizo- and phytodegradation Groundwater, vadose zone, wetlands, wastewater, and leachate contaminated with water-soluble contaminants (east.g., chlorinated solvents, MTBE, explosives, other organic contaminants, salts, and some elements).
(1) Phyto- or solar pumping, phytohydraulic control, and phytohydraulic barriers (also biobarriers) (1) Field proof of principle: Populus spp. (TCE, PCE, MTBE, and CCl4)
(2) Control of soil and landfill leaching (2) Concept not proven
(3) 'Pump and tree', phytoirrigation, or other institute treatment ex situ (3) Proposed and undergoing testing: (a) pine (Pinus spp.) (TCE and by-products) and (b) Salix spp. (organic solvents, MTBE, petroleum hydrocarbons, and nutrients) (Numbers correspond to those in column 1)
Alkali volume reduction Brines pumped onto halophytes planted in wetlands that accrue or excrete table salt and the smaller volume residual brine transported and disposed of more than economically Deep groundwater or oilfield brines. Wetland halophytes pilot tested in Oklahoma oilfield. No plant residuals: halophytes fed to cattle as a source of salt afterward toxicity testing of plants
Rhizofiltration: phytofiltration, blastofiltration, phyto- or biosorption, biocurtain, biofilter, contaminant uptake, and epuvalization Compounds taken up, rapidly sorbed, or precipitated by roots (rhizofiltration) and young shoots (blastofiltration) or sorbed to fungi, algae, and leaner (biosorption mainly to prison cell walls involving electrostatic attraction and germination of complexes). Marine algae possess large quantities of biopolymers (polysaccharides, uronic acids, and especially sulfated polysaccharides) that bind heavy metals. 10–60% dry weight of institute may be accumulated metals Wetlands, wastewater, landfill leachates, surface water, and pumped groundwater contaminated with metals, radionuclides, organic chemicals, nitrate, ammonium, phosphate, and pathogens. Plant roots or shoots, aquatic plants, or algae, all alive or dead, are added to or contained in wetlands, tanks, flowing h2o channels, or columns. Disposal of residuals unresolved. US practise is to dispose of residuals in hazardous waste matter landfills. Conceptually, metals sorbed to prison cell walls may exist acrid-extracted. Economic recovery of metals needs to be explored. Field proof of concept: sunflower (Helianthus annuus) at Chernobyl, Ukraine (Cs and Sr), and field airplane pilot, Ashtabula, Ohio, for U. Proof of concept for phytosorption: aquatic plants (Salvinia spp. and Spriodela spp.) (Cr and Ni from wastewater and Pb, Cu, Atomic number 26, Cd, and Hg), algae (several metals), and marine algae (Sargassum Au: 40% of the algal dry weight). Proof of concept for rhizofiltration: sunflower (Helianthus annuus) and Indian mustard (Brassica juncea) (Lead, Cr, Mn, Cd, Ni, Cu, U(vi), Zn, and Sr)
Phytovolatilization: biovolatilization andphytoevaporation Volatile metals and organic compounds are taken up, sometimes re-speciated (metals), and transpired. Some recalcitrant organic compounds are more than hands degraded in the temper merely most multimedia transfers require a take a chance assessment before testing Soils, sludges, wetlands, and groundwater contaminated with Se, tritium, As, Hg, k-xylene, chlorobenzene, tetrachloromethane, trichloromethane, trichloroethane, and other chlorinated solvents. Field proof of principle: Se from wastewaters and soil. Field proof of concept: tritium from groundwater. Current technical consensuses: (1) TCE volatilization has not proven meaning to date but site risk assessments are required to be certain. The risk of volatilization of other organic pollutants has not been explored. (2) Transgenic plants volatize Hg in the lab but redeposition from the temper makes field applications less viable.
Phytoextraction (including chelator induced): phytoaccumulation, phytoconcentration, phytotransfer, hyperaccumulation, and phytomining Contaminants taken up with water by cation pumps, assimilation, and other mechanisms and usually translocated above ground. Harvested shoots or roots put in hazardous waste landfills or could be smelted afterward volume reduction by incineration or composting. Hyperaccumulation is approximately 100 times normal plant accumulation of elements and is 0.01% by dry weight for Cd and other rare elements, 0.1% for well-nigh heavy metals, and 1% for Fe, Mn, and other mutual elements Extraction from soil of metals, metalloids, radionuclides, perchlorate, BTEX, PCP, curt-chained aliphatic and other organic compounds non tightly bound to soils (although phytodegradation of inorganic and organic molecules is more sustainable). US practice is disposal of residuals in hazardous waste product landfills but Ni smelting is feasible. Composting to reduce disposal volume conceptualized. Pilot field-testing eastern US: unproven at six sites with Pb using B. juncea merely proven at two sites with Zn and Cd using Thlaspi caerulescens. Phytomining Ni: 2 US locations and testing in Albania and South Africa. Field proof of concept: Ni, Zn, Sr, Cs (see following warning), and Cd from long-term application of sludges using Brassicaceae hyperaccumulators in UK; Mariupol and Chernobyl regions, Ukraine; and Pennine Mountains, UK (plus Ag, Al, Co, Fe, Mo, and Mn). Failed 2 evaluations using chelators for Pb; thus questionable for Cr, Cs, and other tightly bound elements. New lab proof of concept now required for Pb and other tightly bound elements. Proof of concept: 1993–95 for Cd, Ni, Zn, Cu, Se, B, and other elements. Bench testing: at arid western US site for Cr, Zn, Hg, Ag, and Se using Salix 10, Kochia scoparia, and Brassica napus and perchlorate using wetland halophytes.
Phytoslurry Enzymatically active found material ground and slurried with wastewater, contaminated soil, or sediment Lab proof of concept: wastewater, soil, or sediment contaminated with DNT and TNT
Phytophotolysis Contaminant translocated from soil or h2o into leaves and broken downward by photolysis Proposed concept for soil, wastewater, wetlands, and groundwater contaminated with RDX
Phytostabilization: biogeochemical stabilization, biomineralization, phytosequestration, and lignification (1) Revegetation to prevent erosion and sorbed pollutant send Soil, mine tailings, wetlands, and leachate pond sediments contaminated with metals, phenols, anilines, some pesticides, tetrachloromethane, trichloromethane, and other chlorinated solvents
(2) Plants control pH, soil gases, and redox that crusade speciation, precipitation, and sorption to form stable mineral deposits (effects of ecosystem succession unknown on long-term stability and thus sustainability) (1) All-encompassing applications: revegetation grasses established for different metals dominated wastes in Great britain and U.s.a. erosion prevention handbooks available for many countries
(three) Humification, lignification, and covalent or irreversible binding of some organic compounds are expected (2) Bench proof of concept: for stabilization of some pesticides, phenols, and anilines
(3) Lab proof of concept: for Pb and Cr6+(six)a (the numbers correspond to those in column 2)

BTEX, benzene, toluene, ethyl benzene, and xylene; DCE, dichloroethane; DDT, ddt; DNT, dinitrotoluene; HCA, hexachloroethane; HMX, octahydro-one,iii,v,7-tetranitro-one,3,five,seven-tetraazocine; MTBE, methyl tert-butyl ether; NB, nitrobenzene; NT, nitrotoluene; PAHs, polycyclic aromatic hydrocarbons; PCBs, polychlorinated biphenyls; PCE, tetrachloroethene; PCP, pentachlorophenol; RDX, hexahydro-1,three,5-trinitro-1,3,5-triazine; TCE, trichloroethene; TNT, 2,iv,half dozen-trinitrotoluene; VC, vinyl chloride.

If heterotrophs are solely responsible for the metabolism or mineralization of organic contaminants and the accumulation of metals and other elements using local accumulations of nonliving organic thing and oxidized inorganic compounds, these processes are part of the centrolineal field of 'bioremediation'. However, when photoautotrophs are involved in treating contaminants by

•

actively releasing organic thing during growth, maintenance, and senescence that increase the number and biomass of heterotrophs;

•

selectively favoring specialized microorganisms that dethrone or accumulate contaminants by pumping oxygen into the root zone, releasing exudates, or depositing secondary metabolites during root die-back in the rhizosphere to favor aerobic, facultative, or anaerobic organisms with enzymatic activity for the secondary products released or deposited; and

•

transporting pollutants into agile microbial zones by evapotranspiration, blockage of flows, or other ways.

These processes are a vital part of phytoremediation. Depending on the various interactions of photoautrophs and heterotrophic microbial communities and the contaminant transformations involved, these processes are known as 'phytostimulation', 'rhizo(sphere) degradation', 'rhizosphere bioremediation', or 'plant-assisted bioremediation' (see Table one ).

Distinction of bioremediation from phytostimulation is of import in at least three cases. Get-go, some heterotrophs sustainably derive carbon and energy from the degradation of organic contaminants. Second, anthropogenically synthesized organic or oxidized inorganic chemicals added to a contaminated site could temporarily gratis bioremediation from natural photograph- or chemoautotrophic synthesis long enough by cometabolism to achieve some cleanup. Tertiary, chemoautrophs synthesizing biomass from inorganic compounds to provide organic carbon and free energy for heterotrophs conceivably could be used in sustainable bioremediation. If any amendments and cofactors are obtained and added sustainably, and then these bioremediation processes are sustainable. The most common amendment is fertilizer, used primarily to majority upward plant biomass and thus increase microbial biomass and activity in the rhizosphere.

Redundant ecological engineering of both establish and microbial processes in remediation is ordinarily the sustainable and successful approach. In practise, distinctions between phyto- and bioremediation are simply important for some specific contaminants at dissimilar sites. Unlike direction approaches and techniques are required when microbial heterotrophy versus photoautotrophy dominates. Critical rates of pollutant control, uptake, storage, and metabolism, whether microbial or botanical, ascertain whether plant or microorganism management techniques must be applied. When disquisitional rates for microbial and botanical uptake and transformation are comparable, both techniques should exist applied simultaneously for engineering redundancy and ecological resilience.

One of the most significant advances in phytoremediation is that greenish liver metabolism is much more important in waste product direction than early biotechnology research revealed. Sandermann starting time coined the term 'dark-green liver' to convey the swell similarity between institute and mammalian sequestration and metabolism. So great is the similarity that many view found metabolism more than alike to mammalian metabolism than to bacterial metabolism. In fact, many cardinal metabolic processes first evolved in early on cyanobacteria and bacteria and were carried forrad, sometimes without evident purpose, into higher forms of life nowadays today, including vascular plants and mammals. Only for future xenobiotic and highly complex hazardous wastes, the about sustainable applications may need to concentrate on use of the most highly evolved enzymatic systems available simply in plants and animals. In part, bacteria versus college forms of life accept evolved different survival strategies. Microbes are nowadays in not bad numbers, well-nigh ubiquitous on this planet, commonly passively mobile, more than adjustable, and capable of evolving apace. Thus, a toxic insult will kill many microorganisms but the species volition ordinarily survive, possibly even the rigors of outer space. If the die-off is extensive or long term, new protections may evolve by choice of the fittest.

Plants are normally rooted in place and are much fewer in number. Thus, plants may have evolved greater numbers of metabolic proteins used to detoxify insults in place, than microorganisms evidently require for survival. Plants are different from animals in the lack of (i) an immediate flight response and (ii) excretion of transformation products. Animals tend to excrete transformation products, whereas plants tend to accumulate some transformation products in vacuoles or betwixt layers of molecules in cell walls. Plant transformation products are accumulated and could exist released into the environment upon death and lysis of found cells.

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Factors affecting the growth and survival of fungi in wood (fungal ecology)

Robert A. Zabel , Jeffrey J. Morrell , in Woods Microbiology (Second Edition), 2020

Substrate (food sources)

As heterotrophs, fungi and most bacteria crave a nutrient source or substrate that provides iii major needs.

(a)

Energy from the oxidation of carbon compounds.

(b)

A puddle of metabolites for the synthesis of the wide range of compounds needed for growth and evolution (chitin, glucans, nucleotides, enzymes, proteins, lipids, etc.).

(c)

Required vitamins, minor elements, CO2, and nitrogen.

An indirect substrate requirement is the absenteeism of various growth inhibitors and the physical access of microbial enzymes to the required substrate constituents.

Microbial carbon nutrition has get a large and complicated subject. Essentially all carbon-based compounds are subject to microbial degradation under some conditions. This subject will be discussed in greater particular in Chapter 5 on metabolism.

As a generalization, fungi are eucaryotes that appear to have evolved as scavengers of plant remains (selective for carbohydrates and low pH conditions). Leaner, as procaryotes, are the major consumers of animal bodies (selective for proteins and neutral pH conditions). The same generalization holds for the diseases caused by bacteria and fungi. There are, however, many exceptions or crossovers where bacteria assault living plants or their remains or where fungi set on animals.

Many fungi can degrade and utilise carbohydrates including cellulose, simply only the wood-inhabiting decay fungi—a few k species at best—are able to dethrone and utilize carbohydrates in the cellulose-hemicellulose-lignin complex comprising the wood jail cell wall.

The monosaccharide d-glucose is utilized past essentially all fungi and is a mutual carbon source in many cultural media. Galactose, mannose, and fructose are used by many fungi, but announced to be initially converted to glucose-six-phosphate and so follow the same metabolic pathways as glucose in the respiration or fermentation processes.

The oligosaccharides maltose, cellobiose, and sucrose are also expert carbon sources for many fungi. Malt extract is a preferred medium for many wood disuse fungi, providing both glucose and vitamins.

Many fungi are able to utilize polysaccharides, such as cellulose, starches, and various hemicelluloses. The presence of small-scale amounts of lignin every bit a bulwark or shield around clusters of the carbohydrate components apparently drastically limits enzyme access and microbial set on to the modest grouping of wood inhabiting micro-organisms. Some bacteria likewise dethrone wood, merely at a very slow rate.

Optimum nutrient sources vary widely for both fungi and leaner. This variation is exploited in bacterial identification keys and was too explored for cultural identification of fungi. Determining optimum nutrient sources and growth conditions for wood-inhabiting micro-organisms will assistance develop a better understanding of probable organismal successions (discussed in Chapter 11) in various stem invasions, heartrot developments, and preferential attack of various woods products.

Hydrogen ion concentration (pH)

Fungi commonly have a pH for optimum growth and a minimum and maximum at which no growth occurs. In full general, the optimum is skewed toward the maximum value in a way similar to cardinal temperature requirements. In contrast to vegetative growth, sporulation and spore germination have more restrictive pH tolerances. As a substrate factor, external pH primarily affects substrate availability, rates of exo-enzymatic reactions, exo-enzyme stability, cell permeability, extracellular components and solubility of minerals and vitamins. Information technology has little influence on the pH of cytoplasm. Hydrogen ion concentration does not always bear on a unmarried characteristic and low levels may alter exo-enzyme action, while loftier levels might inhibit minor metal solubilities. These furnishings sometimes produce bimodal pH growth curves. In general, fungi grow best within a pH range of three–6, while many bacteria and actinomycetes abound best at a pH of 7, simply both groups ofttimes alter the pH of their substrate. Some optimum pH values for wood disuse fungi are: Heterobasidion annosum four.vi–4.ix; Cerocorticium (Merulius) confluens 4.0; and K. sepiarium, Fomotopsis rosea, Serpula lacrimans, and Coniophora (Cerebella) puteana at iii.0. Many plant pathogens have optimal growth within a pH range of 5–6.5. Wood-decomposable Basidiomycetes accept pH optima ranging from 3 to six. Brown rotters have the lowest optima (around pH 3). Wood stain fungi are highly pH sensitive and their growth often diminishes or (ceases) as pH exceeds 5. Forest decay fungi lower the pH of wood during the decay process, and this characteristic forms the ground of several chemical indicator tests proposed for detecting incipient decays in pulpwood and utility poles (Eslyn, 1979). Woods of many species are already lightly acidic.

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Bioprospecting of endophytic fungi for antibacterial and antifungal activities

Bhat Mohd Skinder , ... Abdul Hamid Wani , in Phytomedicine, 2021

1.i Endophytic fungi

Fungi are heterotrophs belonging to the eukaryotic group, which are establish-like organisms without chlorophyll that absorbs nutrients through its cell wall. They reproduce by spores and take a filamentous body called "thallus" (mycelium) composed of branching, microscopic tubular cells chosen "hyphae." Fungi are "biotrophs" when they get food from a living host, "saprotrophs" (saprobes, saprophytes) when they feed on a expressionless host, and "necrotrophs" when they infect and kill a living host to obtain their nutrients ( Carris, Lilliputian, & Stiles, 2012). Equally per molecular data, fungi are nearly more than i billion years quondam (Parfrey, Lahr, Knoll, & Katz, 2011), just fossil show record shows them every bit about 3.v billion years old (Redecker, Kodner, & Graham, 2000). At to the lowest degree 99,000 fungal species have been labeled, and new species being designated at the rate of 1200 per twenty-four hour period (Blackwell, 2011; Kirk, Cannon, Minter, & Stalpers, 2008). As per Hawksworth (2001), there are around 250,000 plant species worldwide considering there are six species of fungal per plant, which accounts for a total of 1.5 1000000 fungal species (i.five   ×   250,000). However, information technology is estimated per molecular studies that there are around 6 1000000 soil fungi at the global level (Taylor et al., 2014). Fungi are ubiquitous-occurring heterotrophic organisms, often revealing symbiotic traits including mutualistic, antagonistic, or neutral symbiosis with dissimilar autotrophic organisms (Saar, Polans, Sørensen, & Duvall, 2001). A fungus is associated with both plants and animals. However, there is an ancient relationship between fungi and plants. Fungi on the establish surface are called "epiphytic fungi," and fungi residing within the plant tissues are called "endophytic fungi." Thus, these are fungal microorganisms that spend their entire or part of their life cycle residing inter- and/or intracellularly, inside the healthy plant tissues without causing credible signs of any diseases (Petrini, 1991).

The term "endophyte" is from the Greek words "endo" or "endon" significant within and "phyte" or "phyton" pregnant plant, which was introduced past de Bary (1866), for fungi inhabiting plant tissue. An endophytic fungus lives in "mycelial" form in clan with plant tissue. Thus, for a fungus to be termed endophyte, information technology should at to the lowest degree establish its "hyphae" in living tissue (Kaul et al., 2012). These are omnipresent in every found, whether a plant found in the dessert or a plant found in a hotspot of global biodiversity. Medicinal plants of Western Ghats of Bharat (a hotspot of global biodiversity) are a repository of diverse population of endophytic fungi (Raviraja, 2005). There is more than one endophyte inhibiting 300,000 plant species existing on Earth (Strobel & Daisy, 2003). They include all asymptomatic symbiotic associates of the eukaryotic group Plantae (Azevedo, Maccheroni, Pereira, & de Araújo, 2000; Bacon & White, 2000; Stone, Bacon, & White, 2000; Wilson, 1995), which is a vascular plant, or grasses all host endophytes (Zang, Becker, & Cheng, 2006). Fungi, bacteria, actinomycetes, and mycoplasma were found to exist an endophytic organism in plants (Bandara, Seneviratne, & Kulasooriya, 2006). These are one of the most important elements in plant microecosystems, which have pregnant influences on growth and development of the host plants. However, a few of these plants take been studied for endophytic biology, but research on endophytes today are much more than progressed and advanced. Different aspects of endophytic organisms could be investigated, to accept a master and elementary thought about the endophytic fungal population of particular plant species. At that place is an immense demand of biodiversity, taxonomic, and molecular-based studies that include genomics, proteomics, and transcriptomics. The focus of studies also includes endophytes producing "secondary metabolites" and their various activities, antimicrobial, antifungal, antimalarial, antioxidant, anticancer, insecticidal, and pesticidal. The secondary metabolites were called natural products, start recognized past Sachs (1874). "Mycophenolic acid" isolated from Penicillium glaucoma is the first crystalline fungal secondary metabolite discovered by Gosio (1896). They have an ability to promote the accumulation of secondary metabolites of the host plants, which influenced the quantity and quality of drugs (Chen et al., 2016). Although endophytes play a very important function in affecting the quality and quantity of the crude drugs through a particular fungus-host interaction, our cognition virtually the verbal relationships betwixt endophytic fungi and their host plants is nevertheless very limited. In that location is need to sympathize such relationships for the promotion of crude drug product (Faeth & Fagan, 2002). In the present context, bioprospecting of endophytic fungi from unlike medicinal plants for different bacterial and fungal strains in respect of antibacterial and antifungal activities are existence highlighted that could possibly exist used in the pharmaceutical industry to revolutionize the medicinal world in a sustainable way.

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Marine Enzymes Biotechnology: Production and Industrial Applications, Part III - Application of Marine Enzymes

S. Parte , ... J.S. D'Souza , in Advances in Food and Diet Inquiry, 2017

four.3 Fungi

Fungi are eukaryotic heterotrophs existing as single filaments or aggregates in almost all sorts of niches such equally oceans, coastal areas, estuaries, on state, or mangrove swamps. Results of high-throughput sequencing methods predict v.one one thousand thousand fungal species to exist on world, of which marine fungi comprise >  1500 species. Marine fungi thrive in the sea either every bit obligates or in facultative modes, exist equally complimentary-floating entities or society onto driftwood, sand grains, shells, sponges, algae, mollusks, corals, plants, fish, etc. (Blackwell, 2011; Bonugli-Santos et al., 2015), and are supposedly the fundamental players in marine habitat. Despite a significant role played especially past the endophytic marine fungi with respect to the bioactive secondary metabolite/chemical compound product (such as terpenoids, steroids, quinones, phenols, and coumarins) possessing antioxidant, antiviral, antibacterial, anticancer, antidiabetic, antifungal, antiprotozoal, antituberculosis, antiinflammatory activities, insecticidal properties, and applications in pharmaceutical and agrochemical industry, these entities occupying the oceans remain under-explored (reviewed by Hamed et al., 2015; Li et al., 2014).

Marine fungi secrete several enzymes (Tabular array 3; xylanases, lignin peroxidases, manganese peroxidases, and laccases) that also cause breakdown of circuitous compounds such as industrial toxins and crude oil components (Atalla et al., 2010). Extremophilic microorganisms produce alkaliphilic enzymes (proteases, cellulases, lipases, and pullulanases) which have tremendous industrial applications (Horikoshi, 1999). Proteases are enzymes with application in detergent formulation industry and are of commercial significance. Proteases and lipases also find their applications in dairy industry. Xylanases are majorly produced by fungi and find prominence in fields of food, feed, beverage, and fabric industries and in waste product treatment. Another group of enzymes with diverse applications are cellulolytic enzymes required in carbohydrate and ethanol fermentation, detergents, chemicals, lurid and paper, fabric manufacture, fauna feed, and food manufacture (Moubasher et al., 2016).

Table 3. Details of Marine Enzymes Derived From Fungus

Enzyme Enzyme Source Enzyme Function and/or Application Reference
Element of group i protease Scopulariopsis spp. Useful in detergent formulations Niyonzima and More (2014)
Alginate lyase, amylase, cellulase, chitinase, fructosyl-amino-oxidase, fucoidanase, glucanase, galactosidase, glucosidase, glucosaminidase, hexose-aminidase, inulinase, keratinase, ligninase, lipase, nuclease, phytase, polygalacturonase, protease, speroxide dismutase, and xylanase Pestalotiopsis sp., Aureobasidium pullulans N13d, Penicillium janthinellum P9, Debaryomyces hansenii C-xi, Aspergillus oryzae, Penicillium canescens, Trichoderma aureviride KMM4630, Aspergillus awamori BTMFW032, Penicillium melinii, Flavodon flavus, etc. Implicated in Fungal Marine Biotechnology (Biotechnology—hydrolytic and oxidative enzymes; Environmental Biotechnology—enzymes degrading cloth effluents and polycyclic hydrocarbons; and Industrial Biotechnology—enzymes related to manufacture of chemical, fuel, food [dairy, baking], drink, agriculture related, textiles, cosmetics, etc.) Bonugli-Santos et al. (2015)
Amylase, cellulase, chitinase, gelatinase, lipase 14 Fungal genera: Penicillium, Aspergillus, Scopulariopsis, Cephalosporium, Humicola, Gymnoascus, Endomysis, Zygorhynchus, Trichoderma, Zalerion, Pleospora, Chaetomium, Phoma, Botryphialophora, unidentified Significant role in remineralization and several industrial applications Smitha, Correya, and Philip (2014)
Laccase, lipase, cellulase, peroxidase, manganese peroxidase Nigrospora species and Arthopyrenia species—marine sponge Trematosphaeria mangrovei Cause breakdown of several ecology compounds, such as industrial toxins and crude oil components; active office in ecological cycles of coastal ecosystem, significance in bioremediation Baldrian (2006), Atalla et al. (2010), Atalla, Zeinab, Eman, Amani, Abd, and AtyAbeer (2013), Li, Singh, Liu, Pan, and Wang (2014), and Passarini, Ottoni, Santos, Lima, and Sette (2015)
l-Glutaminase Marine Beauveria sp. Anticancer properties Sabu, Keerthi, Kumar, and Chandrasekaran (2000)
Uncoupling protein one (UCP1) U. pinnatifida, Hijikia fusiformis, and Sargassum fulvellum Antiobesity enzyme Hamed, Özogul, Özogul, and Regenstein (2015)
Tannase (tannin acyl hydrolase) Aspergillus awamori BTMFW032 Hydrolysis of ester and depside bonds to synthesize gallic acid and glucose; gallic acid is a substrate for production of antibacterial drug trimethoprim, synthesis of propyl gallate, an antioxidant used in food manufacture; and catechin gallates are used in manufacture of instant tea, coffee-flavored soft drinks, flavor improvement in grape wine, beer, and fruit juice clarification, to heighten antioxidant activity of dark-green tea, cleavage of polyphenolics, determination of structure of naturally occurring gallic acid esters Beena (2010)
Cellulase, xylanase, and pectinase Alternaria alternata, Aspergillus terreus, Cladosporium cladosporioides, Emericella nidulans, Fusarium solani, Cochliobolus australiensis Implicated in food, feed, beverage, material industries and in waste treatment; fermentation of sugars and ethanol; for production of detergents, chemicals, pulp and paper; required in textile industry, animal feed, and nutrient industry Moubasher, Ismail, Hussein, and Gouda (2016)

Large-scale production of these enzymes requires optimized culture weather condition, i.due east., bioprocessing in bioreactors (viz., solid-state fermentation) peculiarly for enzymes such as proteases, chitinases, agarases, peroxidases, glucoamylases, superoxide dismutases, lignin peroxidases, chitinases, and glutaminases (Sarkar et al., 2010). Farther, the enzyme needs to exist concentrated, isolated, purified using sophisticated and sequential biochemical and biophysical techniques such every bit ammonium per sulfate precipitation, dialysis, ultracentrifugation, ion-exchange chromatography, acetone atmospheric precipitation, gel and tangential flow filtration, extraction, hydrophobic interaction chromatography, rechromatography, and speed vacuum concentration. Basically, the aim of employing such purification strategies is to obtain maximum yield of the purest form of the enzyme with continuous product recovery, inexpensive in terms of large-scale and continuous-blazon production, and maintaining structural conformation of enzyme to retain its specificity and catalytic action optimum (Bonugli-Santos et al., 2015).

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Other types of spoilage moulds

A.P. Williams , ... Neaves , in Food Spoilage Microorganisms, 2006

eighteen.5.1 Nutrients

Nutritionally, moulds are heterotrophs, in fact having nutritional preferences that are remarkably similar to humans, and hence causing set spoilage of human foods. Past comparison, yeasts are frequently rather fastidious and may be able to assimilate merely a limited range of, for example, sugars. Equally a event yeasts, like bacteria, having limited morphological variety, are characterised largely on substrate utilisation, whereas moulds, having morphological variety merely express nutritional variation, are characterised by colonial and microscopic morphology. One particular characteristic of moulds, used in their characterisation, is the colour of their colony obverse and opposite. This has led to difficulties in recent years, as the quality and purity of manufactured mycological media have improved to the extent that trace metals (mainly copper and zinc) are no longer present at sufficient levels to allow typical growth and the pigments necessary for identification to be expressed. As a result, it is now necessary to amend all mycological media by adding one   ml per litre of trace element solution (i   one thousand ZnSOfour  ·   7HiiO   +   0.5   1000 CuSO4  ·   5HiiO in 100   ml distilled h2o). Where trace metal solution is not bachelor, making media with tap water rather than distilled water is commonly a suitable alternative, although this is not normally acceptable to laboratory accreditation bodies.

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Plastid Genome Evolution

Susann Wicke , Julia Naumann , in Advances in Botanical Research, 2018

4 Are Nosotros Ever Dealing With (Pseudo)genes?

Near sequence data of heterotrophs are obtained from genomic surveys, but additional experimental information are urgently needed to obtain prove for the functionality of ORFs and annotated genes. Basing sentence exclusively on DNA similarity can exist misleading. For instance, the accD cistron varies drastically in length across heterotrophic plants: annotated as an intact gene, information technology ranges from 954   bp in Phelipanche aegyptiaca (Orobanchaceae) (Wicke et al., 2016) to 2094   bp in Monotropa uniflora (Ericaceae) (Braukmann et al., 2017); the median length of accD in heterotrophic plants is 1482   bp. Presumably, all of these accD-similar ORFs are functional, but experimental proof is evidently needed. Plastid gene models thus are hypothetical until validated by species-specific expression or protein data. Studies of factor expression deliver of import evidence and are powerful in finding the correct coding region. However, some caution should be used with the estimation of these data. Gene expression does not necessarily mean that a gene product volition also be active on the protein level, which, ultimately, represents the level of function. For case, a case study centring around several recent holoparasitic species of Orobanchaceae showed that rbcL is expressed but not translated into a functional peptide in some parasites (Randle & Wolfe, 2005).

Frequently, variations of "the gene … is highly diverged and probably non-functional" can be read in inquiry reports, but, to our knowledge, the bodily functional space of plastid genes, i.e., the extent to which nucleotide substitutions and indels tin be tolerated on the functional (peptide) level, has non notwithstanding been determined—neither for photosynthesis genes nor for housekeeping genes. In the absence of clear criteria as to when a gene should be annotated as a pseudogene based on Dna evidence, information technology is the responsibleness of the individual researcher to determine the category into which a factor in question belongs. There is as much unawareness of the functional realm of plastid proteins as there is on the extent of putative researcher bias in annotating plastid genes of unusual departure. For case, assuming that a gene of a parasite has an intact ORF that is 35% shorter and 96% divergent in sequence compared with its equivalent in a phylogenetically closely related autotroph. How many researchers would allocate this gene as "functional" or equally "pseudogene"? Some sure would ask for bear witness of gene expression, but when no RNA-course materials of this plant (at its various developmental stages) are available, should this genomic region then improve be left unannotated? Certainly non—only peradventure we could add an annotation note pointing others to this form of uncertainty.

An inspection of available sequences in GenBank shows that differences in factor annotation most often indeed pertain to categorizing genes as "intact" or "pseudogenes". However, it also seems as if different views exist as to when a gene is "absent". While one researcher might classify face-to-face stretches of less than 10 amino acids every bit insignificant evidence for the retention of a pseudogene fragment, another researcher would annotate this region equally pseudogene. In effect, downstream analyses, like the reconstruction of ancestral gene content, will carry over discrepancies, no affair their origin, with the potential to severely influence the direction of data interpretation. Determining the degree of researcher bias in annotating plastomes of heterotrophs is hard. Hence, peers should be commended for their candour to acknowledge that sometimes their categorization of genes every bit intact or pseudogenes may exist incorrect in the absence of functional information.

Does notation quality affair? We think then. Many aspects in the field of heterotrophic plant plastomics centre on questions like which genes are lost, when that loss occurred, and in which lineages and how chop-chop. These questions cannot be answered with conviction if there are reservations well-nigh the accuracy of the underlying information. Ideally, the community would work towards refining existing annotations past calculation cistron expression and poly peptide data. Because the scarcity of some textile paired with the remoteness of habitats where some heterotrophs abound, broadly complementing existing plastome sequences with new experimental data seems unrealistic. Some other measure would be to implement best-practice standards with recommendations for assembly, factor finding, and annotation procedures and to analyze criteria for categorizing pseudogenes. Although many researchers might welcome such standardized procedures, how should the customs handle published data that may not comply with these recommended procedures? Devising methods or best-exercise procedures with a battery of tested software and recommendations for stringency settings or transmission curation may likewise contribute to overcoming note biases. Likewise, when taxon sampling is sufficiently dense, the error of the reconstructed events of pseudogenization or loss-of-function deletions can be minimized to some extent. Nonetheless, it remains the risk to infer events at deeper nodes in a phylogenetic tree and thus in a common ancestor when really these events were independent (or vice versa).

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