Microbial Biomass Composition Research Articles

Микробная биомасса – биоресурс для получения функциональных пищевых ингредиентов (обзор)

Microbial biomass is a promising source of essential macro- and micronutrients to be used in the food industry, e.g., protein, vitamins, essential amino acids, polysaccharide, etc. This article reviews scientific publications on the properties and composition of microbial biomass as a source of functional ingredients, its biological effectiveness, production methods, and composition.
 The review covered research articles published in 2005–2021 and indexed in eLIBRARY.RU, Google Scholar, Scopus, Elsevier, and PubMed. It relied on such general scientific methods as analysis, generalization, and systematization.
 Saccharomyces cerevisiae yeast and Aspergillus mycelial fungi appeared to be the most popular research objects. Most studies concentrated on the chitin-glucan-mannan complex of cell walls and protoplasmic biovaluable protein. Others featured the biocatalytic conversion of microbial polymers with the transfer of biologically valuable components into an enzyme-accessible state. Bioactive ingredients of microbial origin could be divided into sorbents, immunomodulators, neurotransmitters, antioxidants, and anticarcinogenics.
 Microbial fermentolysates are a potential source of bioactive compounds for functional foods. However, the medical and biological properties of their minor bioactive components remain understudied while fermentolysates can yield new functional products fortified with essential amino acids and low-molecular bioactive peptides.

Influence of microbial biomass content on biodegradation and mechanical properties of poly(3-hydroxybutyrate) composites

Biodegradation rates and mechanical properties of poly(3-hydroxybutyrate) (PHB) composites with green algae and cyanobacteria were investigated for the first time. To the authors knowledge, the addition of microbial biomass led to the biggest observed effect on biodegradation so far. The composites with microbial biomass showed an acceleration of the biodegradation rate and a higher cumulative biodegradation within 132 days compared to PHB or the biomass alone. In order to determine the causes for the faster biodegradation, the molecular weight, the crystallinity, the water uptake, the microbial biomass composition and scanning electron microscope images were assessed. The molecular weight of the PHB in the composites was lower than that of pure PHB while the crystallinity and microbial biomass composition were the same for all samples. A direct correlation of water uptake and crystallinity with biodegradation rate could not be observed. While the degradation of molecular weight of PHB during sample preparation contributed to the improvement of biodegradation, the main reason was attributed to biostimulation by the added biomass. The resulting enhancement of the biodegradation rate appears to be unique in the field of polymer biodegradation. The tensile strength was lowered, elongation at break remained constant and Young’s modulus was increased compared to pure PHB.

Absence of canonical trophic levels in a microbial mat.

In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."

Cellular and extracellular C contributions to respiration after wetting dry soil

Wetting of dry soil triggers a pulse of microbial respiration that has been attributed to two broad mechanisms: (1) recycling of microbial cellular carbon (C), and (2) consumption of extracellular organic C made available to microbes by wetting. We evaluated these two mechanisms by measuring cumulative CO2 release, changes in the size and chemical composition of microbial biomass, and water-extractable organic carbon (WEOC) concentrations following artificial wetting of soil sampled from two depths at each of seven sites across California spanning a range of geologic parent materials. In samples collected from surface soil (0–10 cm depth), we found that cumulative CO2 release after wetting in the laboratory was most strongly correlated with microbial biomass. In these samples, the relative abundance of trehalose—a putative microbial osmolyte—decreased from 25% (SD = 12) to 16% (SD = 7) of the chloroform-labile fraction of the microbial biomass after wetting. This suggested a role for osmolyte consumption in generating the respiration pulse. In subsoil (40–50 cm depth, or sampled at contact with rock), however, the cumulative CO2 release after wetting was unrelated to microbial biomass and more strongly related to WEOC. The concentrations of selected microbial biomass constituents (e.g. trehalose and amino acids) in WEOC were negligible (< 1%), suggesting that cell lysis was not important in generating WEOC in this study. The amount of WEOC relative to total organic C was greatest in subsoil, and negatively related to ammonium oxalate-extractable Fe (Pearson’s R = 0.42, p < 0.01), suggesting a role for soil mineralogical properties in controlling WEOC release. Together, these findings suggest that microbial cellular C and extracellular C jointly contribute to the respiration pulse, and that their relative contribution depends on depth.

Immediate fire-induced changes in soil microbial community composition in an outdoor experimental controlled system

Short-term fire-induced changes to the soil microbial community are usually closely associated to fire severity, which essentially consists in the fire-induced loss or decomposition of organic matter above ground and below ground. Many functional processes and soil properties, including plant recolonization and soil microorganism activity, depend on fire severity. Seven days after burning, we evaluated the impact of two fire severities (low and high) on basic soil properties and the microbial communities in an outdoor experimental controlled system composed of six forest soil monoliths. The magnitude of change in microbial community was far greater than the change in physical and chemical soil properties. Total N was the only selected soil property that significantly varied depending on fire severity. The severely burned soils experienced significant changes in overall microbial biomass composition and phylogenetic composition of bacterial communities in comparison with control plots. Immediately after the fire, in fact, phyla and genera such as Acidobacteria-Gp4 or Bacteroidetes-Ohtaekwangia were much more abundant in the control monoliths. On the other hand, Firmicutes or Proteobacteria (e.g. Firmicutes Paenibacillus, Proteobacteria Phenylobacterium) were relatively more abundant in the monoliths burned with high severity in comparison with the low severity burned ones. Overall, the effect of fire on soil microbial communities was greater in the high severity burned monoliths than in the low severity burned ones. We concluded that in Mediterranean forest ecosystems, fire significantly alters soil bacterial composition depending on its severity.

Estimation of biomass composition from genomic and transcriptomic information.

Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.

Estimation of biomass composition from genomic and transcriptomic information

SummaryGiven the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genomescale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.

Soil properties and not inputs control carbon : nitrogen : phosphorus ratios in cropped soils in the long term

Abstract. Stoichiometric approaches have been applied to understand the relationship between soil organic matter dynamics and biological nutrient transformations. However, very few studies have explicitly considered the effects of agricultural management practices on the soil C : N : P ratio. The aim of this study was to assess how different input types and rates would affect the C : N : P molar ratios of bulk soil, organic matter and microbial biomass in cropped soils in the long term. Thus, we analysed the C, N, and P inputs and budgets as well as soil properties in three long-term experiments established on different soil types: the Saria soil fertility trial (Burkina Faso), the Wagga Wagga rotation/stubble management/soil preparation trial (Australia), and the DOK (bio-Dynamic, bio-Organic, and “Konventionell”) cropping system trial (Switzerland). In each of these trials, there was a large range of C, N, and P inputs which had a strong impact on element concentrations in soils. However, although C : N : P ratios of the inputs were highly variable, they had only weak effects on soil C : N : P ratios. At Saria, a positive correlation was found between the N : P ratio of inputs and microbial biomass, while no relation was observed between the nutrient ratios of inputs and soil organic matter. At Wagga Wagga, the C : P ratio of inputs was significantly correlated to total soil C : P, N : P, and C : N ratios, but had no impact on the elemental composition of microbial biomass. In the DOK trial, a positive correlation was found between the C budget and the C to organic P ratio in soils, while the nutrient ratios of inputs were not related to those in the microbial biomass. We argue that these responses are due to differences in soil properties among sites. At Saria, the soil is dominated by quartz and some kaolinite, has a coarse texture, a fragile structure, and a low nutrient content. Thus, microorganisms feed on inputs (plant residues, manure). In contrast, the soil at Wagga Wagga contains illite and haematite, is richer in clay and nutrients, and has a stable structure. Thus, organic matter is protected from mineralization and can therefore accumulate, allowing microorganisms to feed on soil nutrients and to keep a constant C : N : P ratio. The DOK soil represents an intermediate situation, with high nutrient concentrations, but a rather fragile soil structure, where organic matter does not accumulate. We conclude that the study of C, N, and P ratios is important to understand the functioning of cropped soils in the long term, but that it must be coupled with a precise assessment of element inputs and budgets in the system and a good understanding of the ability of soils to stabilize C, N, and P compounds.

Comparison of different pilot scale bioreactors for the treatment of a real wastewater from the textile industry

Wastewater from textile industry usually undergoes activated sludge biotreatment ahead of refining treatments, final discharge or reuse. To identify the most effective bioreactor typology for the secondary treatment of a wastewater resulting from a textile industry of the Biella district (Italy), four pilot units characterized by a different configuration and fluid dynamics (i.e., Bioflotation ®, Fixed Bed Biofilm Reactor (FBBR), flow-jet aeration and standard aerobic sludge reactors) were operated in parallel, inoculated with the same microbial consortium and fed with identical streams of wastewater discharged from wet textile processes of the industy. COD, TC and non-ionic surfactants were monitored in effluents of the compared bioreactors working under continuous mode and the cultivable heterotrophic microorganisms prevailing in each of them were isolated and characterized as the end of the study. The results demonstrated that the air supply system greatly influenced the treatment efficiency which reached the highest value in the case of Bioflotation ® and FBBR technology. A highly specialized bacterial biomass mostly composed by strains of the Pseudomonas, Stenotrophomonas and Ochrobactrum genera was isolated in such reactors, thus suggesting that a direct correlation between reactor configuration, decontamination performances and microbial biomass composition exist.

Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment

Biota can be described in terms of elemental composition, expressed as an atomic ratio of carbon:nitrogen:phosphorus (refs 1-3). The elemental stoichiometry of microoorganisms is fundamental for understanding the production dynamics and biogeochemical cycles of ecosystems because microbial biomass is the trophic base of detrital food webs. Here we show that heterotrophic microbial communities of diverse composition from terrestrial soils and freshwater sediments share a common functional stoichiometry in relation to organic nutrient acquisition. The activities of four enzymes that catalyse the hydrolysis of assimilable products from the principal environmental sources of C, N and P show similar scaling relationships over several orders of magnitude, with a mean ratio for C:N:P activities near 1:1:1 in all habitats. We suggest that these ecoenzymatic ratios reflect the equilibria between the elemental composition of microbial biomass and detrital organic matter and the efficiencies of microbial nutrient assimilation and growth. Because ecoenzymatic activities intersect the stoichiometric and metabolic theories of ecology, they provide a functional measure of the threshold at which control of community metabolism shifts from nutrient to energy flow.

Biochemical analysis of soil organic matter and microbial biomass composition—a pilot study

Biochemical composition of both intracellular (biomass) and extracellular soil organic matter was determined after extraction with 0.5 M K 2SO 4. Extractable carbon, hexoses, pentoses, total reducing sugars, ninhydrin-reactive nitrogen (NRN), proteins and DNA content were colorimetrically determined. The objective of the pilot study was to examine the information potential included in newly measured biochemical characteristics, their environmental variance and the relationships with main soil properties. Correlation analysis and PCA showed independence between biochemical parameters and physico-chemical properties of the soil. Thus, the parameters characterising biochemical composition of the soil biomass and extracellular matter seem to bring new information about the soils beyond the physico-chemical parameters. They also seem to reveal a more detailed view on microbial biomass or extracellular organic matter pool than C bio or C ext alone, respectively. The variance, which occurred in biochemical characteristics, also displayed a high discrimination potential between the defined soil categories. Three types of indices were newly proposed: index I (“substrate quantity index”)—the biomass-specific amount of the extracellular organic compounds, index II (“immobilisation ratio”)—the portion of the organic compound immobilised in microbial biomass, and index III (“substrate quality index”)—the extracellular organic compound content related to extracellular organic carbon. The indices displayed a higher potential than both soil biotic and abiotic parameters to discriminate soil characters and soil types.

Evaluation of supplements to enhance nutrient supply and milk production of cattle fed diets based on elephant grass ( Pennisetum purpureum) using a mathematical model

A previously developed dynamic model of digestion and absorption of nutrients in cattle fed sugarcane-based diets ( Dijkstra et al., 1996a) was modified to evaluate the effect of various supplements on the supply of nutrients and milk production of dairy cows fed diets based on elephant grass ( Pennisetum purpureum). The predicted nutrient supply was examined by varying the fractional passage rates of fluid and solid material, and by varying the microbial biomass composition. Besides, model predictions were compared with observations of faecal NDF flow, rumen ammonia and VFA concentrations, and milk production. The milk production is predicted from the simulated availability of glucogenic, lipogenic and aminogenic nutrients and the total amount of energy available, to indicate which type of nutrient is most limiting. The behaviour of the model with respect to overall stability and sensitivity to parameter perturbation was generally considered to be satisfactory. The simulations showed the relevance of careful estimation of fractional passage rates. In comparison with experimental observations, the model behaviour is unsatisfactory with respect to the prediction of rumen Am and VFA concentrations. Model predictions appeared adequate to predict faecal NDF flow. However, model predictions on milk production were not always adequate. The simulations suggest that the low availability of glucose and glucose precursors is the factor most limiting milk production on unsupplemented elephant grass-based diets. The paucity of firm data on elephant grass-based diets prevents the use of this model for prediction purposes in practice.

Application of quantitative IR spectral analysis of bacterial cells to acetone–butanol–ethanol fermentation monitoring

Clostridium acetobutylicum ATCC 824 was grown under three different acetone–butanol–ethanol (ABE) fermentation conditions: (1) strictly anaerobic conditions with vegetative inoculum; (2) semi-anaerobic conditions with vegetative inoculum; and (3) strictly anaerobic conditions with spore inoculum. Semi-anaerobic fermentation with vegetative inoculum and strictly anaerobic fermentation with spore inoculum produced solvents at high level. Strictly anaerobic fermentation with vegetative inoculum showed an “acid crash”, i.e. produced mainly acids and did not switch to predominant solvent production. The content of carbohydrates, nucleic acids, proteins and lipids in Clostridium cells during the fermentation were evaluated from the mid-IR spectra. The content of nucleic acids decreased with process time, and the lipid content increased, corresponding to ceasing growth and formation of the toxic fermentation products. It was shown that the physiological states of either solvent production or acid crash are reflected in the microbial biomass composition, which can be assessed by IR spectroscopy.

Carbon and ninhydrin‐reactive nitrogen of the microbial biomass in rewetted compost samples

We studied the applicability of the so‐called fumigation‐extraction method for microbial biomass carbon and ninhydrin‐reactive nitrogen to evaluate the stabilization of rewetted compost samples. Dried samples of composts of widely different composition, sampled at the initial, thermophilic, mesophilic and curing stages of composting, were remoistened to 50% of water content and incubated at 25°C for 5 days before analysis. In rewetted raw materials, microbial biomass carbon (Bc) ranged from 11,296 to 41,601 μg/g and significatively decreased in samples of increasing stabilization reaching only 2704–5837 μg/g in rewetted mature composts. The percentage of Bc with respect to total organic carbon (C) varied from 2.5 to 9.5% in starting materials, but was lower than 1.7% in all the end products. Ninhydrin‐reactive N of the microbial biomass (BNIN) showed the same trend that Bc, ranging from 504 to 2044 μg/g in raw material samples, declining in samples of increasing composting time and achieving rather close values in the end products (from 90 to 303 μg/g). The percentage of BNIN respect to total N was higher in raw material samples (2.0–9.8%), with final values lower than 1.1%. The Bc and BNIN showed a strong correlation (r=0.99, P<0.001) with a regression coefficient (20.1) in good agreement with those found for soils. Incubation at high temperature (53 °C) negatively influenced the content of Bc and BNIN at all composting stages and had little, if any, effect on the chemical composition of microbial biomass. Results of this work show that the application of methods for the measure of microbial biomass C and ninhydrin‐reactive N in soil to rewetted composts gives valuable information on the degree of stabilization achieved by the product.

Correlation between cell composition and carbon conversion efficiency in microbial growth: a theoretical study

As the macromolecular composition of microorganisms varies during their life cycle it was asked whether, and to what extent such changes exert any influence on substrate consumption, i.e. growth yield and carbon conversion efficiency, respectively. This question was dealt with in a theoretical study by use of the Y APT max -concept. The growth substrates considered were methanol, acetate and glucose; the latter was assumed to be assimilated via both the glycolytic and the oxidative hexosemonophosphate pathway. Five fictitious biomasses were used which were altered in their proportion of polysaccharides, proteins, lipids, RNA and DNA. As a result, only small variations in the individual “biomass formulae” were obtained. On the basis of the energy balances for the syntheses of all cell constituents it was found that variations in the macromolecular composition of microbial biomass have only a slight effect on carbon conversion efficiency, amounting to maximally 3%. From the material balances it could be calculated that the upper, solely metabolism-determined limit of carbon conversion efficiency is 85% for substrates assimilated glycolytically via phosphoglycerate; for gluconeogenetic substrates, the upper limit was 75%. These limits are essentially determined by carbon loss on the way to amino acid syntheses.