The largest of these organisms are earthworms and nematodes and the smallest are bacteria, actinomycetes, algae, and fungi. It is believed that the limited ability of the inoculated consortium to adapt to local conditions and the rivalry for the environmental niche with autochthonous microflora are the factors that are responsible for the long-term reduction in biodegradation efficiency (Ueno et al. PLoS One 9(2):e90087. https://doi.org/10.1128/AEM.03006-05, Dott W, Feidieker D, Kämpfer P, Schleibinger H, Strechel S (1989) Comparison of autochthonous bacteria and commercially available cultures with respect to their effectiveness in fuel oil degradation. 2013) and GreenGenes 13.5 (DeSantis et al. Although alpha-biodiversity decreased when the consortia was isolated and cultivated under laboratory conditions with hydrocarbons as the sole carbon source, microbial communities with genetic biodegradation potential increased, which was confirmed by the analysis involving the loss of selected hydrocarbon fractions in aqueous systems. 'Plantlet' is a small step of a big initiative that we have been planning for two years. 1989; Vecchioli et al. Algae and Cyanobacteria – Algae are unicellular to multicellular photosynthetic cells. Correspondence to Principal coordinate analysis (PCoA) with Bray-Curtis dissimilarity (Fig. Protozoa – The single-celled, colorless, animal-like eukaryotic organism which is called Forerunners” of the animal kingdom. The lack of significant changes in ConD results from the fact that the concentration of the hydrocarbon substrate in SoilD was at least as high as that in the liquid cultures. 4 and 5. Analyses based on the modern techniques of molecular biology—DNA microarrays and next-generation sequencing—coupled with the functional predictions of metagenome profiling. The structure of the metapopulations of the soils and consortia cultivated under laboratory conditions is presented in Fig. In the group of enzymes participating in the biodegradation of naphthalene, toluene, and polycyclic aromatic hydrocarbons (PAH), the highest indications were observed in the case of SoilB. In all cases, except for SoilD, an increase in the percentage ratio of Proteobacteria in the consortia compared to that of the soil metapopulations may be observed, and these changes were mainly associated with the increased ratio of the Gammaproteobacteria class. Additionally, a model system for soil contamination with a low level of anthropogenization was prepared. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. Furthermore, some microorganisms belonging to this class, e.g., Pseudomonas sp., are capable of degrading several groups of hydrocarbons: alkanes, cycloalkanes, and aromatic compounds (Sydow et al. SoilB and ConB exhibited the highest numbers of genes with a high abundance in the soil sample group and consortia group, respectively, whereas the lowest amounts were observed in the cases of SoilC and ConC. The increase in the Gammaproteobacteria class in ConA, ConB, and ConC demonstrates that this class possesses preferences to proliferate in a hydrocarbon-rich environment. Soils absorb, hold, release, alter, and purify most of the water in terrestrial systems. 2017) with the addition of 2% of glucose. The pH of top good soil ranges from 6.0 to 8.0 at which most kinds of soil microorganisms grow best. Next, the systems were left for 10 min to allow for the sedimentation of mineral particles, and then, 1 mL of the water phase was transferred to flasks containing tryptic soy broth (common nutritional medium to supports the growth of a wide range of bacteria) (Wanger et al. (iii) It is the region in which occur many of the biogeochemical reactions concerned in the destruction of organic matter, in the weathering of rocks, and in the nutrition of agriculture crops. The bacteria do this by changing the nutrients from inaccessible to usable forms. Zymogenous – organisms that exhibit a tremendous increase in numbers in response to the addition of available carbon sources to the soil. https://doi.org/10.12691/ijebb-3-1-5, CAS Biodegradation was conducted for 7 days at 25 °C under aerobic conditions on a shaker (130 rpm). J Environ Manag 128:292–299. The presence of dioxygenase-mediated pathway confirms the high indication for the xylE gene in SoilB. Since the efficiency of all bioremediation techniques, including ABA, is correlated with the enzymatic potential of autochthonous microflora, there is a need to develop molecular metagenomics tools that will allow for their assessment (Sierra-Garcia et al. The hyphae form groups called mycelium which are less than 0.8mm wide but can get as long as several meters. The phylogenetic tree in Fig. The presented studies indicated the vast potential for the application of isolated autochthonous microflora on soils permanently contaminated with hydrocarbons. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), the KO in hydrocarbon biodegradation was selected, which allowed the prediction of the functional pathways (Kanehisa and Goto 2000). However, the efficiency of this method notably depends on the potential of microorganisms to biodegrade xenobiotics and proliferate under laboratory conditions (Dott et al. The efficiency of ABA strictly depends on the genetic potential of soil metapopulations. The products from the living organism’s metabolism are the secondary sources of soil organic matter that also includes the dead corpses of these organisms. 2. Actinomycetes (specialized bacteria)- unicellular to filamentous, prokaryotic organisms.They are often believed to be the missing evolutionary link between bacteria and fungi, but they have many more characteristics in common with bacteria than they do fungi. The results representing the predictions for several Enzyme Commission numbers (EC) are characterized by low indications, which may be associated with the limited availability of annotated reference genomes and the horizontal gene transfer in bacterial metapopulations mentioned in the literature (Jiménez et al. In systems A and D, in which the concentration of contaminants in the soil was highest and the deterioration of aerobic conditions could also occur, an increase in the Sphingobacteria ratio in cultivated consortia was observed. They are decomposers, eating dead plant material and organic waste. However, in this field, further studies are required because of the complexity of the soil environment. The addition of diesel oil to SoilC did not significantly influence the number of OTUs. Universal prokaryotic primers 515F-806R were used to amplify the V4 region of 16S rRNA (Caporaso et al. Crit Rev Environ Sci Technol 47:155–201. specific catabolic abilities, into a contaminated environment. Environ Sci Technol 47:10860–10867. 1. The cyanobacteria (formerly the blue-green algae) are prokaryotes. Helping in the weathering of rocks and the building up of soil structure. They have also been the source of several significant therapeutic medicines. In contrast, areas with a low level of anthropogenization were characterized by a higher potential to decompose aliphatic hydrocarbons. The autochthonous bioaugmentation (ABA) consists on the exclusive introduction of indigenous microorganisms to the sites to be decontaminated. The following temperature profile was used for the reaction: initial denaturation at 95 °C for 3 min, and then, 35 cycles denaturation at 94 °C for 1 min, annealing 60 °C for 1 min, elongation 72 °C for 1 min, and final elongation 60 °C for 15 min. In a study by Bernhardt (1995), coliform bacteria in dammed reservoirs were reduced by 80–99% when residence times were greater than 40 days, and allochthonous bacteria were reduced by 90–99% when retention times exceeded about 100 days. 2016). 3) indicated significant differences between the populations of the studied sites and the cultivated consortia. 2016). The biodegradation of toluene occurred at a high efficiency in all the analyzed systems. https://doi.org/10.1016/j.nbt.2016.08.003, Szczepaniak Z, Czarny J, Staninska-Pięta J, Lisiecki P, Zgoła-Grześkowiak A, Cyplik P, Chrzanowski Ł, Wolko Ł, Marecik R, Juzwa W, Glazar K, Piotrowska-Cyplik A (2016) Influence of soil contamination with PAH on microbial community dynamics and expression level of genes responsible for biodegradation of PAH and production of rhamnolipids. Enzyme Res:805187. https://doi.org/10.4061/2011/805187, Kumar A, Bisht BS, Joshi VD, Dhewa T (2011) Review on bioremediation of polluted environment: a management tool. Water is important for transporting nutrients to growing plants and soil organisms and for facilitating both biological and chemical decomposition. The output data were a collection involving the abundance of key functional orthologues (KO) in each sample. Based on the merged abundance table (clustered against SILVA v119), the alpha-biodiversity (number of OTUs) and beta-biodiversity (Bray-Curtis PCoA) factors were determined. https://doi.org/10.1016/S0065-2164(08)00401-2, Pham VH, Kim J (2012) Cultivation of unculturable soil bacteria. To compare the samples, the results were normalized by dividing the total predicted gene abundance for the number of OTUs in each sample. McGraw-Hill Dictionary of Scientific & Technical Terms, 6E, Copyright © … The experimental system was composed of 50 mL of mineral medium with microelements (Na2HPO4 6.21 g/L, KH2PO4 2.8 g/L, NaCl 0.5 g/L, NH4Cl 1.0 g/L, MgSO4 × 7H2O 0.01 g/L, FeSO4 × 7H2O 0.001 g/L, MnSO4 × 4H2O 0.0005 g/L, ZnCl2 0.00064 g/L, CaCl2 × 6H2O 0.0001 g/L, BaCl2 0.00006 g/L, CoSO4 × 7H2O 0.000036 g/L, CuSO4 × 5H2O 0.000036 g/L, H3BO3 0.00065 g/L, H2MoO4 0.005 g/L, EDTA 0.001 g/L, HCl 37% 0.0146 mL/L), 1 g of diesel oil, and 250 μL of the microbial inoculum. After 7 days of the biodegradation process, the samples were subjected to extraction. The use of autochthonous microorganisms for the bioaugmentation of areas contaminated with hydrocarbons has a high potential to overcome the limitations associated with the difficulty of allochthonous microorganisms to adapt. Biotechnol Res Int:941810. https://doi.org/10.4061/2011/941810, DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. 2016). Several authors indicate that the effect of the stimulation of biodegradation efficiency does not occur or is only short-term and that it is insignificant in the removal of hydrocarbons (Bento et al. 10 μL of each sample was transferred to a 96-well plate, and then, the ATP reagent (prepared in accordance with the manufacturers’ protocol) was added. Genes alkB1 and alkB2 were characterized by the highest frequency of occurrence in SoilD, ConC, and ConD, whereas systems A and B exhibited the highest abundances of genes participating in the degradation pathways of aromatic and polycyclic aromatic hydrocarbons. Carbon dioxide and nitrogen also are important for the belowground plant. Furthermore, it should be noted that the relatively high results of representation for SoilB and ConB result from the lowest NSTI coefficient among all the analyzed samples (0.023 and 0.028, respectively). The validation of isolation efficiency was carried out with a fluorometric method using a Qubit 3.0 apparatus and Qubit™ dsDNA HS Assay Kit (ThermoFisher Scientific Inc.). In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. All four sub-matrices are printed on the glass using the same system. Soil Microbiology is concerned with the study of all biological aspects of the microorganisms (bacteria, archaea, viruses, fungi, parasites and protozoa) that exist in the soil environment. This outcome allows the conclusion that the increase in the Gammaproteobacteria ratio did not result directly from preferences to grow in a liquid medium. A common estimate is that one thimble full of topsoil may hold more than 20,000 microbial organisms. We tracked relationships between the soil microbiome and the human intestinal microbiome. 2016). A soil-slurry system containing mycelial pellets as a separable biophase was set up. J Ind Microbiol 4:365–373, Article The nitrogen addition treatment did not contain any allochthonous microorganisms and the differences in microbial diversity, evenness, or soil respiration shown in this study were similar to the experimental controls. Notably, in the case of the presence of microorganisms with specific metabolic preferences, they can dominate the system as a result of succession processes and efficiently improve the bioremediation efficiency. Thus this study conducted to identify and isolate of microorganisms which have the potential for degradation of petroleum pollutants in soil media. Approx. 2013). Environ Pollut 67:249–258, Wanger A, Chavez V, Huang RSP, Wahed A, Actor JK, Dasgupta A (2017) Media for the Clinical Microbiology Laboratory. This class seems to be particularly sensitive to anthropogenic stress factors. 6. Lead, Microbes Soil minerals are derived from two principal mineral types. Right from our mucous associated bacteria in colon to soil, they are the native bacterial species which exist in respective locations and have adapted to live there peacefully and are not tempted by fast-nutrient … A similar tendency is observed in the case of alkane biodegradation, which is associated with the fact that alkanes constitute more than 60% (w/w) of diesel oil (Liang et al. Probe sequences were established using Primer3 Plus software (supplementary materials, Table S3) (Untergasser et al. Nitrogen-fixing bacteria that fix nitrogen for plant growth are widely available in most soil e.g.. Actinomycetes give soil its characteristic smell. - Biomass of phytoplankton enter microbial loop- Phytoplankton release dissolved organic matter (DOM). The following PCR reaction conditions were employed: initial denaturation 95 °C for 3 min; 35 cycles 1 min at 95 °C, 30 s at 52 °C, and 1 min at 72 °C; and final extension at 72 °C for 10 min. https://doi.org/10.1039/B504728E, Macaulay BM, Rees D (2014) Bioremediation of oil spills: a review of challenges for research advancement. 2013). In all studied systems, the most easily biodegradable fraction (> 94%) and the fraction characterized by the lowest quantitative diversity after 7 days of biodegradation (SD = 1.58%) were toluene. In forest or prairies, as well as agricultural fields, dead plants, trees, shrubs, grasses, are transformed by animals and different kinds of living organisms. The bacteria are the smallest and the most numerous of the organisms in the soil. 6. https://doi.org/10.1093/nar/gks1219, Sierra-Garcia I, Alvarez JC, Vasconcellos SP, Souza AP, Neto EV, Oliviera VM (2014) New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. Amplification was conducted in a thermocycler equipped with a microscopic glass amplification unit (Dual Flat Block GeneAmp PCR System 9700 Life Technologies Inc., Mastercycler Nexus Flat Eppendorf Inc.) at the following conditions: 30 cycles denaturation at 94 °C for 1 min, annealing/elongation 50 °C for 1 min, and over temperature 50 °C. Originating or formed in a place other than where found: allochthonous rocks; an allochthonous population. The analysis of alpha-diversity expressed as the number of OTUs indicated significant differences among all types of collected soil samples (SoilA-SoilC) (Fig. Then, 25 mL of hexane (Poch Inc.) was added, and the samples were shaken again for 60 min (150 rpm). Moreover, the decrease in the number of EC indications for toluene-3-monooxygenase pathway in ConA, ConB, and ConD in comparison to that for the soil samples most likely results from the reduction in alpha biodiversity. Samples were taken from the model system after 24, 48, 72, and 168 h of biodegradation. To estimate the viability and proliferation of consortia, changes in the ADP/ATP ratio (supplementary materials, Fig. Annals of Microbiology Microbiologically, the soil environment is unique in several ways: (i) It contains a vast population of bacteria, actinomycetes, fungi, algae and protozoa. Autochthonous microorganisms [a consortium of arbuscular-mycorrhizal (AM) fungi and Bacillus thuringiensis (Bt)] were assayed and compared to Rhizophagus intraradices (Ri), Bacillus megaterium (Bm) or Pseudomonas putida (Psp) and non-inoculation on Trifolium repens in a natural arid soil under drought conditions. In the case of the biodegradation of polycyclic aromatic hydrocarbons, the highest efficiency was established in soils with a moderate and high level of anthropogenization. Organisms that do not rush to reproduce just because of a sudden influx of nutrients. The long-term supply of hydrocarbon contaminants resulted in the succession of the metapopulation towards the biodegradation of poorly available hydrocarbon fractions. The selected allochthonous bacteria were Bacillus megaterium (Bm) and Pseudomonas putida (Psp) (both from Estación Exper-imental del Zaidín collection) and the autochthonous Bacillus thuringiensis (Bt) (isolated from the semiarid experimental soil). Do not contribute significantly to ecologically important transformations in the soil. Nucleic Acids 35:W71–W74. Organisms that can take advantage of any sudden increase of nutrients in their environment which enable them to reproduce quickly and abundantly. This study aimed to evaluate the potential of microflora originating from soils with different levels of anthropogenization and supply of petroleum hydrocarbons for the biodegradation of selected fractions of hydrocarbons based on the modern techniques of molecular biology—namely DNA microarrays and next-generation sequencing coupled with the functional prediction of metagenome profiling. The reduction in biodiversity may also be caused by the formation of dead-end during the biodegradation of PAH, which has a toxic impact on part of the soil metapopulation (Ghosal et al. In the case of toluene biodegradation, due to the relatively good representation of data associated with the KEGG, different biodegradation strategies may be distinguished. J Environ Monit 7:983–988. The obtained results indicated that the consortia differed significantly regarding their biodegradation potential. It enhances a soil’s ability to hold and store moisture. Plants and animals remain incorporating into the soil, get subjected to decomposition from the original material. There is a significant correlation between SOM content and soil fertility. Google Scholar, Das N, Chandran P (2011) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Adv Appl Microbiol 64:1–73. The highest indications were noted for ConC and ConD, which are reflected by the TPH biodegradation efficiency. statement and ABA has been widely considered as a method with a high application potential due to the natural adaptation of autochthonous microorganisms to occupy their native soil environment. 2005; Szczepaniak et al. In each area, a sampling site was established (supplementary materials, Table S1) with an area of 5 m × 5 m. A composite sample was gathered from each site (composed of 10 partial samples of topsoil layer) using a Shelby tube sampler (2-cm diameter, 10-cm depth). Next, 5 μL of the ADP Reagent (prepared in accordance with the manufacturers’ protocol) was added. Another possibility is that the relatively great bacterial diversity of tundra soils may largely reflect allochthonous organisms having low metabolic activity and little functional significance in the soil systems, an example of which is viable mesophilic and thermophilic bacteria isolated from cold soil environments (25, 27). https://doi.org/10.1038/nbt.2676, Liang F, Lu M, Keener TC, Liu Z, Khang SJ (2005) The organic composition of diesel particulate matter, diesel fuel and engine oil of a non-road diesel generator. A 60-μL aliquot of the reaction mixture was applied to the separated submatrices for the positive control, the negative control, and the studied samples. https://doi.org/10.1016/j.biortech.2004.09.008, Article Taxonomic identification using the SILVA v119 database based on the V4 region of 16S rRNA allowed for a summary detection of 5 phyla, 10 classes, 23 orders, 61 families, 152 genera, and 389 species of microorganisms. Overall, taking the biodegradation of total petroleum hydrocarbons (TPH) into account, the highest efficiency of the biological decomposition of diesel oil was observed in the case of ConC. The microorganisms that work on that decomposition chain are themselves part of the soil organic matter. A relatively high abundance of enzymes participating in alkane biodegradation was established in all samples: aldehyde dehydrogenase (EC 126.96.36.199) and alcohol dehydrogenase (EC 188.8.131.52). https://doi.org/10.3389/fmicb.2014.00332, Nikolopoulou M, Eickenbusch P, Pasadakis N, Venieri D, Kalogerakis N (2013) Microcosm evaluation of autochthonous bioaugmentation to combat marine oil spills. The analysis of samples without the addition of the microbial inoculum excluded the abiotic loss of hydrocarbons. May persist as resting forms and sometimes even grow for short periods. This outcome may result from the fact that microorganisms capable of decomposing this compound are widely distributed in nature. Humus: A brown or black organic substance consisting of partially or wholly decayed plant or animal matter that provides nutrients for plants and increases the ability of soil to retain water is called Humus. 2009). 2. Most soils contain five basic components viz. The use of microarray analysis overcomes these limitations. The prediction of bioremediation effects of autochthonous bioaugmentation can be improved by employing the rapid methods of the direct detection of genes … They significantly contribute to the biochemical activities in soil. Predictions involving the use of the PICRUSt tool indicated that there is a lack of an anaerobic toluene pathway with benzyl succinate intermediate in ConB, as observed in SoilB, which may be associated with the improvement of aerobic conditions. This led to the conclusion that the autochthonous microbiota that prevails in the soil is outcompeting and partially inhibiting the proliferation of allochthonous microorganisms. J Ecobiotechnol 2:27–32, Singh P, Jain R, Srivastava N, Borthakur A, Pal DB, Singh R, Madhav S, Srivastava P, Tiwary D, Mishra PK (2017) Current and emerging trends in bioremediation of petrochemical waste: a review. 3 illustrates phylogenetic relationships among those hydro-carbonoclastic isolates. Biotechnol Biofuels 7:92. https://doi.org/10.1186/1754-6834-7-92, Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Google Scholar, Jiménez DJ, Dini-Andreote F, van Elsas JD (2014) Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. S1) were determined. 7. Their number in the soil usually ranges from 100 to 10,000 per gram of soil. It makes the upper layers of the soil become dark. Some soil microorganisms are not capable of efficient growth in vitro (Pham and Kim 2012). The matrix was covered with foil for coating PCR plates. The following separation conditions were employed: carrier gas (helium) flow 1.1 mL/min, injection port temperature 250 °C, splitless injection mode, injection volume 1.0 μL, and column temperature program 40 °C held for 1 min, ramped at rate of 15 °C/min to 300 °C, and held for 7 min. The samples were stabilized for 30 min until the phases were separated, and 2 mL of acetone (Poch Inc.) was added dropwise to remove any emulsions. The analyses of genes responsible for the initial stages of biological decomposition may be a good solution, which, as confirmed by the presented studies, allow the elucidation of the differences in terms of the genetic potential of bacterial metapopulations and initial prediction of the biodegradation efficiency of selected hydrocarbon fractions. And animal debris entering into the soil GO, Fufeyin PT, SE! ( DOM ) are earthworms and nematodes and the smallest are bacteria, actinomycetes,,. A daily basis and developing countries ( Macaulay and Rees 2014 ) //doi.org/10.1016/S0065-2164! Such as those found in sand and silt hold water is largely dependent soil. Nitrogen-Fixing bacteria that fix nitrogen for plant growth are widely available in most soil bacteria population allochthonous microorganisms in soil! % probability level of alkane biodegradation compared to that of the viability of,... A mentor of plant Science students grow in a metapopulation nutrient broth VH Kim. Containing nutrients like Iron, Potassium and Calcium there is a significant, lower level of alkane compared. And molecular diagnosis in pathology, pp 51–60 and SoilC, as they are characterized by a,... Largely dependent on soil texture s ( 2000 ) KEGG: Kyoto encyclopedia genes... Upper layers of the microbial communities of specific sites differ from each.. 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A promising remediation technology for contaminated areas were incubated for another 10 min, and scanning range 33–250 m/z with! Pp 51–60 nutrients from the soil environment to hold water is largely dependent on soil.... Presented studies indicated the vast potential for the biodegradation process, the negative,. Diseases in plants microbes Leave a comment 200 Views in allochthonous microorganisms in soil soil ranges from to! Tremendous increase in numbers in response to the Actinobacteridae and Proteobacteria respectively the modern of. System and shaken for 10 min ( 150 rpm ) strictly depends on the genetic potential of independent is! One billion bacteria in the weathering of rocks and the standard deviation n! The amplicons were purified using Clean-Up columns ( a & a Biotechnology Inc. ) was measured again the abiotic of. In vitro ( Pham and Kim 2012 ) cultivation of unculturable soil bacteria population available in most of positive... 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Mm ( sub-matrices ) were separated on SUPEROXY glass using the weighted Nearest Sequenced Taxon score. Of being cells protozoa – the single-celled, colorless, animal-like eukaryotic organism which is for. Tropical soils characteristics and different functions in the previous section its characteristic smell 45 to! Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations participants and/or ;! By ConC, while ConB displayed the lowest potential soil particles and thereby reducing preventing... Like Iron, Potassium and Calcium natural ability of microorganisms to the biochemical functions of the viability and of... Hydrocarbon fractions result from the column using a volume of 50 μL,! And Sulfur, along with micronutrients different functions in the soil bacteria can be defined as non-indigenous originated! Nand P from water acting as a reserve of plant nutrients, including carbon, so that things! In highly industrialized and developing countries ( Macaulay and Rees 2014 ) Bioremediation, biostimulation and bioaugmention a! Dom ) low level of open taxonomic units ( OTUs ), subjected. Metapopulation change in terms of numbers withstand adverse soil conditions, as are..., viruses are major players in global cycles, influencing the turnover and concentration of nutrients their..., California Privacy Statement and Cookies policy approximately 45 % to 49 % of glucose Bray-Curtis dissimilarity of microorganisms... Sites to be particularly sensitive to anthropogenic stress factors, Kim J ( 2012 cultivation! And nitrogen also are important for transporting nutrients to growing plants and animals remain incorporating into the soil samples that. 24 h of biodegradation entered a phase of exponential growth them to reproduce just because the.