Nutrient Use and Remineralization

Walter K. Dodds , in Freshwater Ecology, 2002

STOICHIOMETRY OF HETEROTROPHS, THEIR FOOD, AND NUTRIENT REMINERALIZATION

Heterotrophs remineralize nutrients when they are in excess 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 consume, the nutrients in the food they eat can frequently exceed the amount needed.

As an example of the stoichiometric effects of the carbon requirement for both growth and respiration, consider a fish that is able to convert only 10% of the carbon it 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 106:16:1 mol of C:N:P, only 1/10th of the C, N, and P can be used for growth. The excess N 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 study of the requirements for ratios of nutrients, the stoichiometry of heterotrophs, and the composition of their food.

Most 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, as discussed previously. Bacteria can retain N increasingly as the C:N ratio of the dissolved, organic material consumed decreases; thus, net remineralization is high at low C:N ratios (Fig. 16.10).

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

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

The dissolved organic carbon available to bacteria may be poor in N and P, and they may need to meet 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 (e.g., remineralization) can be tied to stoichiometry of organisms (Elser et al., 1996). For example, copepods have a higher N:P ratio than the cladoceran Daphnia (Fig. 16.11). The low N:P ratio of Daphnia means that it has a relatively high P requirement for growth (Sterner, 1993). This requirement can lead 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 N: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 function.

FIGURE 16.11. Data showing N:P ratio of Daphnia is lower than that of copepods, indicating different nutrient 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 Environment (Second Edition), 2008

2.3.3.1 Overview

Heterotrophs represent a major sink for primary production, and thus a critical part of the marine N cycle. In the pelagic realm, there have been attempts to estimate zooplankton grazing (both micro- and macro-zooplankton) using two major enzymatic approaches: activities of digestive enzymes (especially proteases in the case of N) (e.g., Gonzalez et al., 1993) and the activity of GDH, the key 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 also been given to the digestive enzymes of benthic heterotrophs, though this has been related more to assessing digestive acclimation and food quality than to quantifying rates. Digestive enzymes have been examined in connection with food supply and feeding rates (e.g., Mayer et al., 1997), and to help determine what materials might be degraded by different species in different environments (Roberts et al., 2001).

Figure 32.3. 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 Future Directions in Biocatalysis, 2007

1 INTRODUCTION

Heterotrophs such as 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 contrary, autotrophs such as plant cell and microalgae are rare to be utilized for biotransformations, and investigation is necessary because they are environment-friendly catalysts: they absorb carbon dioxide to generate oxygen using solar energy. Among photosynthetic organisms, microalgae are expected to form a new group of biocatalysts because of the high growth rates compared to plant cells. In this chapter, reduction, oxidation, and hydroxylation using algae are introduced. Environmental 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 bacteria) live by consumption of biomass or nonliving organic matter. Due to the chemical composition of biomass (disregarding skeletal material or support structures) across all heterotrophs falls within a relatively narrow range, carnivores that feed on other heterotrophs are assimilating approximately the same mixture of elements that they will need in order to synthesize their own biomass (skeletal material and support structure typically pass through the gut unassimilated). Hence, their food quality is high. Detritivores also benefit 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 as nutrients that would alter the balance typical of living biomass.

Unlike heterotrophs, photoautotrophs assimilate elements separately from water or, if they are rooted vascular plants, from sediments. For example, carbon is derived from H2CO3 and related inorganic carbon forms dissolved in water, and phosphorus is taken up separately as phosphoric acid that is dissolved in water. 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:nutrient ratio under nutrient-depleted conditions. Thus, autotrophs face greater challenges than carnivores in assembling the necessary ratios of elements to synthesize biomass, but also herbivores (and bacteria) can experience imbalances of elements.

The approximate ratios of elements that are characteristic of autotrophic biomass have been extensively studied. Characteristic ratios of carbon to nitrogen and phosphorus are often the greatest focus of analysis. Because 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 N, or RNA which is rich in P). The importance of C:N: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 about 106:16:1. Thus, the nutrient status of a phytoplankton community can be judged to some degree from the elemental ratios. For example, a phytoplankton community suffering phosphorus deficiency may show a C:P ratio of 500:1 rather than 106:1, as predicted by the Redfield Ratio for well-nourished phytoplankton. The analysis of elemental ratios for diagnosis of elemental imbalances is termed "ecological stoichiometry" (Sterner and Elser, 2002).

Imbalances in elemental ratios in one trophic level can create imbalances in the diet and thus an inefficient transfer of energy to the next trophic level. This is particularly true between primary producers and herbivores. For example, plants suffering phosphorus scarcity may pass biomass with a high C:P ratio to their grazers. The grazers must then consume extra food in order to obtain the correct balance for the synthesis of their own biomass because of an imbalance of elements in the food. Similarly, an especially low C:P ratio (e.g., 50:1) will provide an oversupply of phosphorus (e.g., when bacteria are consumed), a large part of which is released to the environment 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) as animals and bacteria are generally more nutrient rich than autotrophs. Thus, combining the consumption of a phosphorus-rich food (high quality) with a carbon-rich food (often available in high quantity, e.g., grass), enables a more efficient use of ingested mass than a single food type.

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Phytoremediation

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

Phytoremediation and Other Biotechnologies

'Phytoremediation' is the cleanup or control of wastes, especially hazardous wastes, using green plants. There are many types of phytoremediation, as shown in Table 1 , including the use of phreatophytes to control plumes of groundwater contaminants and contaminated vadose zones. Photoautotrophs, including vascular plants, 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 usually important in direct metabolism, detoxification, and accumulation or storage of pollutants by plants. Glycosylation is a sequestration of contaminant molecules by the addition of a glycosyl group to form a glycoprotein that plant cells can easily transport and store or transform. Not all applications of phytoremediation involve glycoproteins but 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 take up, store, and biochemically degrade or transform organic compounds to harmless by-products, products used to create new plant biomass, or by-products that are further broken down by microbes and other processes to less harmful compounds. Growth and senescence enzymes, sometimes in series, are involved in plant metabolism or detoxification. Reductive and oxidative enzymes may be serially involved in different parts of the plant 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 demonstration: Iowa 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 process to degrade phenols, aniline, and other aromatic contaminants in wastewater. Proof of concept: Rosa spp. cv. Paul's Scarlet (PCBs).
Phytostimulation: rhizodegradation, rhizosphere bioremediation, and plant-assisted bioremediation Plant exudation, root necrosis, and other processes provide organic carbon and nutrients to spur soil bacteria growth by 2 or more orders of magnitude in number; stimulate enzyme induction and cometabolic degradation by mycorrhizal fungi and the rhizomicrobial consortium; provide diverse root zone habitat; and attenuate chemical movements and concentrations. Live roots transfer oxygen to aerobes, and dead roots may support anaerobes or leave 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: (1) 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 pressure 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 (e.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 plant 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)
Brine volume reduction Brines pumped onto halophytes planted in wetlands that accumulate or excrete salt and the smaller volume residual brine transported and disposed of more 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 after 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 bacteria (biosorption mainly to cell walls involving electrostatic attraction and formation 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 plant 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 live or dead, are added to or contained in wetlands, tanks, flowing water channels, or columns. Disposal of residuals unresolved. US practice is to dispose of residuals in hazardous waste landfills. Conceptually, metals sorbed to cell walls may be acid-extracted. Economic recovery of metals needs to be explored. Field proof of concept: sunflower (Helianthus annuus) at Chernobyl, Ukraine (Cs and Sr), and field 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, Fe, 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) (Pb, 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 easily degraded in the atmosphere but most multimedia transfers require a risk assessment before testing Soils, sludges, wetlands, and groundwater contaminated with Se, tritium, As, Hg, m-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 significant 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 atmosphere makes field applications less feasible.
Phytoextraction (including chelator induced): phytoaccumulation, phytoconcentration, phytotransfer, hyperaccumulation, and phytomining Contaminants taken up with water by cation pumps, absorption, and other mechanisms and usually translocated above ground. Harvested shoots or roots put in hazardous waste landfills or could be smelted after 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 most heavy metals, and 1% for Fe, Mn, and other common elements Extraction from soil of metals, metalloids, radionuclides, perchlorate, BTEX, PCP, short-chained aliphatic and other organic compounds not tightly bound to soils (although phytodegradation of inorganic and organic molecules is more sustainable). US practice is disposal of residuals in hazardous waste 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 but proven at two sites with Zn and Cd using Thlaspi caerulescens. Phytomining Ni: two 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 two 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 x, Kochia scoparia, and Brassica napus and perchlorate using wetland halophytes.
Phytoslurry Enzymatically active plant 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 water into leaves and broken down 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 transport 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 cause speciation, precipitation, and sorption to form stable mineral deposits (effects of ecosystem succession unknown on long-term stability and thus sustainability) (1) Extensive applications: revegetation grasses established for different metals dominated wastes in UK and US erosion prevention handbooks available for many countries
(3) 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+(vi)a (the numbers correspond to those in column 2)

BTEX, benzene, toluene, ethyl benzene, and xylene; DCE, dichloroethane; DDT, dichloro-diphenyl-trichloroethane; DNT, dinitrotoluene; HCA, hexachloroethane; HMX, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine; MTBE, methyl tert-butyl ether; NB, nitrobenzene; NT, nitrotoluene; PAHs, polycyclic aromatic hydrocarbons; PCBs, polychlorinated biphenyls; PCE, tetrachloroethene; PCP, pentachlorophenol; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TCE, trichloroethene; TNT, 2,4,6-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 matter and oxidized inorganic compounds, these processes are part of the allied field of 'bioremediation'. However, when photoautotrophs are involved in treating contaminants by

•

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

•

selectively favoring specialized microorganisms that degrade 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 active microbial zones by evapotranspiration, blockage of flows, or other means.

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 1 ).

Distinction of bioremediation from phytostimulation is important in at least three cases. First, 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 free bioremediation from natural photo- or chemoautotrophic synthesis long enough by cometabolism to achieve some cleanup. Third, chemoautrophs synthesizing biomass from inorganic compounds to provide organic carbon and energy for heterotrophs conceivably could be used in sustainable bioremediation. If any amendments and cofactors are obtained and added sustainably, then these bioremediation processes are sustainable. The most common amendment is fertilizer, used primarily to bulk up plant biomass and thus increase microbial biomass and activity in the rhizosphere.

Redundant ecological engineering of both plant and microbial processes in remediation is usually the sustainable and successful approach. In practice, distinctions between phyto- and bioremediation are only important for some specific contaminants at different sites. Different management approaches and techniques are required when microbial heterotrophy versus photoautotrophy dominates. Critical rates of pollutant control, uptake, storage, and metabolism, whether microbial or botanical, define whether plant or microorganism management techniques must be applied. When critical rates for microbial and botanical uptake and transformation are comparable, both techniques should be applied simultaneously for engineering redundancy and ecological resilience.

One of the most significant advances in phytoremediation is that green liver metabolism is much more important in waste management than early biotechnology research revealed. Sandermann first coined the term 'green liver' to convey the great similarity between plant and mammalian sequestration and metabolism. So great is the similarity that many view plant metabolism more akin to mammalian metabolism than to bacterial metabolism. In fact, many fundamental metabolic processes first evolved in early cyanobacteria and bacteria and were carried forward, sometimes without evident purpose, into higher forms of life present today, including vascular plants and mammals. But for future xenobiotic and highly complex hazardous wastes, the most sustainable applications may need to concentrate on use of the most highly evolved enzymatic systems available only in plants and animals. In part, bacteria versus higher forms of life have evolved different survival strategies. Microbes are present in great numbers, almost ubiquitous on this planet, usually passively mobile, more adaptable, and capable of evolving rapidly. Thus, a toxic insult will kill many microorganisms but the species will usually survive, maybe even the rigors of outer space. If the die-off is extensive or long term, new protections may evolve by selection 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 (1) an immediate flight response and (2) excretion of transformation products. Animals tend to excrete transformation products, whereas plants tend to accumulate some transformation products in vacuoles or between layers of molecules in cell walls. Plant transformation products are accumulated and could be released into the environment upon death and lysis of plant cells.

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

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

Substrate (food sources)

As heterotrophs, fungi and most bacteria require a food source or substrate that provides three major needs.

(a)

Energy from the oxidation of carbon compounds.

(b)

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

(c)

Required vitamins, minor elements, CO2, and nitrogen.

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

Microbial carbon nutrition has become 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 detail 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). Bacteria, 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 attack living plants or their remains or where fungi attack animals.

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

The monosaccharide d-glucose is utilized by essentially all fungi and is a common carbon source in many cultural media. Galactose, mannose, and fructose are used by many fungi, but appear to be initially converted to glucose-6-phosphate and then follow the same metabolic pathways as glucose in the respiration or fermentation processes.

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

Many fungi are able to utilize polysaccharides, such as cellulose, starches, and various hemicelluloses. The presence of small amounts of lignin as a barrier or shield around clusters of the carbohydrate components apparently drastically limits enzyme access and microbial attack to the small group of wood inhabiting micro-organisms. Some bacteria also degrade wood, but at a very slow rate.

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

Hydrogen ion concentration (pH)

Fungi usually have a pH for optimum growth and a minimum and maximum at which no growth occurs. In general, the optimum is skewed toward the maximum value in a manner 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. It has little influence on the pH of cytoplasm. Hydrogen ion concentration does not always affect a single characteristic and low levels may alter exo-enzyme activity, while high levels might inhibit minor metal solubilities. These effects sometimes produce bimodal pH growth curves. In general, fungi grow best within a pH range of 3–6, while many bacteria and actinomycetes grow best at a pH of 7, but both groups often alter the pH of their substrate. Some optimum pH values for wood decay fungi are: Heterobasidion annosum 4.6–4.9; Cerocorticium (Merulius) confluens 4.0; and G. sepiarium, Fomotopsis rosea, Serpula lacrimans, and Coniophora (Cerebella) puteana at 3.0. Many plant pathogens have optimal growth within a pH range of 5–6.5. Wood-decaying Basidiomycetes have pH optima ranging from 3 to 6. 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. Wood decay fungi lower the pH of wood during the decay process, and this characteristic forms the basis 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

1.1 Endophytic fungi

Fungi are heterotrophs belonging to the eukaryotic group, which are plant-like organisms without chlorophyll that absorbs nutrients through its cell wall. They reproduce by spores and have a filamentous body called "thallus" (mycelium) composed of branching, microscopic tubular cells called "hyphae." Fungi are "biotrophs" when they get food from a living host, "saprotrophs" (saprobes, saprophytes) when they feed on a dead host, and "necrotrophs" when they infect and kill a living host to obtain their nutrients ( Carris, Little, & Stiles, 2012). As per molecular data, fungi are almost more than 1 billion years old (Parfrey, Lahr, Knoll, & Katz, 2011), but fossil evidence record shows them as about 3.5 billion years old (Redecker, Kodner, & Graham, 2000). At least 99,000 fungal species have been labeled, and new species being designated at the rate of 1200 per day (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 million fungal species (1.5   ×   250,000). However, it is estimated per molecular studies that there are around 6 million 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 different 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 plant 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 apparent signs of any diseases (Petrini, 1991).

The term "endophyte" is from the Greek words "endo" or "endon" meaning within and "phyte" or "phyton" meaning plant, which was introduced by de Bary (1866), for fungi inhabiting plant tissue. An endophytic fungus lives in "mycelial" form in association with plant tissue. Thus, for a fungus to be termed endophyte, it should at least establish its "hyphae" in living tissue (Kaul et al., 2012). These are omnipresent in every plant, whether a plant found in the dessert or a plant found in a hotspot of global biodiversity. Medicinal plants of Western Ghats of India (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 be an endophytic organism in plants (Bandara, Seneviratne, & Kulasooriya, 2006). These are one of the most important elements in plant microecosystems, which have significant influences on growth and development of the host plants. However, a few of these plants have been studied for endophytic biology, but research on endophytes today are much more progressed and advanced. Different aspects of endophytic organisms could be investigated, to have a primary and elementary idea about the endophytic fungal population of particular plant species. There is an immense need 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, first recognized by 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 role in affecting the quality and quantity of the crude drugs through a particular fungus-host interaction, our knowledge about the exact relationships between endophytic fungi and their host plants is still very limited. There is need to understand such relationships for the promotion of crude drug production (Faeth & Fagan, 2002). In the present context, bioprospecting of endophytic fungi from different medicinal plants for different bacterial and fungal strains in respect of antibacterial and antifungal activities are being highlighted that could possibly be 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 Nutrition Research, 2017

4.3 Fungi

Fungi are eukaryotic heterotrophs existing as single filaments or aggregates in almost all sorts of niches such as oceans, coastal areas, estuaries, on land, or mangrove swamps. Results of high-throughput sequencing methods predict 5.1 million fungal species to exist on earth, of which marine fungi comprise >  1500 species. Marine fungi thrive in the sea either as obligates or in facultative modes, exist as free-floating entities or lodge onto driftwood, sand grains, shells, sponges, algae, mollusks, corals, plants, fish, etc. (Blackwell, 2011; Bonugli-Santos et al., 2015), and are supposedly the key players in marine habitat. Despite a significant role played especially by the endophytic marine fungi with respect to the bioactive secondary metabolite/compound production (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 (Table 3; xylanases, lignin peroxidases, manganese peroxidases, and laccases) that also cause breakdown of complex 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 textile industries and in waste treatment. Another group of enzymes with diverse applications are cellulolytic enzymes required in sugar and ethanol fermentation, detergents, chemicals, pulp and paper, textile industry, animal feed, and food industry (Moubasher et al., 2016).

Table 3. Details of Marine Enzymes Derived From Fungus

Enzyme Enzyme Source Enzyme Function and/or Application Reference
Alkaline 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-11, 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 textile effluents and polycyclic hydrocarbons; and Industrial Biotechnology—enzymes related to manufacture of chemical, fuel, food [dairy, baking], beverage, 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 environmental compounds, such as industrial toxins and crude oil components; active role 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 1 (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 industry; 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 enhance antioxidant activity of 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, textile 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 food industry Moubasher, Ismail, Hussein, and Gouda (2016)

Large-scale production of these enzymes requires optimized culture conditions, i.e., bioprocessing in bioreactors (viz., solid-state fermentation) especially for enzymes such as proteases, chitinases, agarases, peroxidases, glucoamylases, superoxide dismutases, lignin peroxidases, chitinases, and glutaminases (Sarkar et al., 2010). Further, the enzyme needs to be concentrated, isolated, purified using sophisticated and sequential biochemical and biophysical techniques such as ammonium per sulfate precipitation, dialysis, ultracentrifugation, ion-exchange chromatography, acetone 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-type production, and maintaining structural conformation of enzyme to retain its specificity and catalytic activity optimum (Bonugli-Santos et al., 2015).

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Other types of spoilage moulds

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

18.5.1 Nutrients

Nutritionally, moulds are heterotrophs, in fact having nutritional preferences that are remarkably similar to humans, and hence causing ready spoilage of human foods. By comparison, yeasts are often rather fastidious and may be able to assimilate only a limited range of, for example, sugars. As a consequence yeasts, like bacteria, having limited morphological variety, are characterised largely on substrate utilisation, whereas moulds, having morphological variety but limited nutritional variation, are characterised by colonial and microscopic morphology. One particular feature of moulds, used in their characterisation, is the colour of their colony obverse and reverse. 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 1   ml per litre of trace element solution (1   g ZnSO4  ·   7H2O   +   0.5   g CuSO4  ·   5H2O in 100   ml distilled water). Where trace metal solution is not available, making media with tap water rather than distilled water is usually 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 We Always Dealing With (Pseudo)genes?

Most sequence data of heterotrophs are obtained from genomic surveys, but additional experimental data are urgently needed to obtain evidence for the functionality of ORFs and annotated genes. Basing judgement exclusively on DNA similarity can be misleading. For instance, the accD gene varies drastically in length across heterotrophic plants: annotated as an intact gene, it 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-like 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 gene expression deliver important evidence and are powerful in finding the correct coding region. However, some caution should be used with the interpretation of these data. Gene expression does not necessarily mean that a gene product will also be active on the protein level, which, ultimately, represents the level of function. For example, 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).

Often, variations of "the gene … is highly diverged and probably non-functional" can be read in research reports, but, to our knowledge, the actual functional space of plastid genes, i.e., the extent to which nucleotide substitutions and indels can be tolerated on the functional (peptide) level, has not yet 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, it is the responsibility of the individual researcher to decide the category into which a gene 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 divergence. For example, 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 classify this gene as "functional" or as "pseudogene"? Some sure would ask for evidence of gene expression, but when no RNA-grade materials of this plant (at its various developmental stages) are available, should this genomic region then better be left unannotated? Certainly not—but perhaps we could add an annotation note pointing others to this form of uncertainty.

An inspection of available sequences in GenBank shows that differences in gene 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 contiguous stretches of less than 10 amino acids as insignificant evidence for the retention of a pseudogene fragment, another researcher would annotate this region as pseudogene. In consequence, downstream analyses, like the reconstruction of ancestral gene content, will carry over discrepancies, no matter 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 admit that sometimes their categorization of genes as intact or pseudogenes may be wrong in the absence of functional data.

Does annotation quality matter? We think so. 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 quickly. These questions cannot be answered with confidence if there are reservations about the accuracy of the underlying data. Ideally, the community would work towards refining existing annotations by adding gene expression and protein data. Considering the scarcity of some material paired with the remoteness of habitats where some heterotrophs grow, broadly complementing existing plastome sequences with new experimental data seems unrealistic. Another measure would be to implement best-practice standards with recommendations for assembly, gene finding, and annotation procedures and to clarify criteria for categorizing pseudogenes. Although many researchers might welcome such standardized procedures, how should the community handle published data that may not comply with these recommended procedures? Devising methods or best-practice procedures with a battery of tested software and recommendations for stringency settings or manual curation may also contribute to overcoming annotation biases. Also, 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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