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Changes in Essential Soil Nutrients and Soil Disturbance Directly Affected Soil Microbial Community Structure: A Metagenomic Approach

Wiryawan Adam, Eginarta Wahyu Satria, Hermanto Feri Eko, Ustiatik Reni, Dinira Layta, Mustafa Irfan

Journal of Ecological Engineering

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2022

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Vol. 23, nr 7

238--245

EN

Soil environment, both biotic (e.g., microbial community) and abiotic (e.g., nutrients and water availability) factors determine soil fertility and health and are directly affected by soil management systems. However, only limited studies evaluate the combined effect of nutrients availability and soil disturbance on the soil bacteria community structure, especially in conventional agricultural practices, on the forests converted to agricultural land. This study aimed to provide a viewpoint of the effect of different soil management systems, i.e., forest soil (natural process) and tilled land, on soil bacteria community structure on forest converted to agricultural land, according to a metagenomics approach. Moreover, each land use was sampled to identify the bacterial community using 16S gene as a biomarker. The sequencing was performed using MinION (Oxford Nanopore Technologies) to read the DNA sequence from each soil sample. Principle Component Analysis (PCA) was performed to comprehend the relationship between availability of nutrients and bacterial diversity. The results revealed that the concentrations of soil micronutrients, such as iron, zinc, and magnesium, were significantly higher in forest soil than in tilled land. According to diversity indices, soil bacteria were more diverse in forest soil than in tilled land. Forest soil had more distinctive taxa than tilled land. Several species comprised the most abundant taxa, such as Candidatus Koribacter versatilis, Candidatus Solibacter usiatus, Rhodoplanes sp., Luteitalea pratensis, and Betaproteobacteria bacterium, were more scarce in tilled land. On the distinctive taxa in each soil sample, Anseongella ginsenosidimutans and Janthinobacterium sp. were the most abundant species in forest and tilled land, respectively. According to PCA analysis, soil management system affected the soil micro-and macronutrients also microbial community structure between forest and tilled land. In conclusion, soil management influences the essential nutrient content and bacterial community structure of soil. Better management should be adopted to maintain soil quality near forest soil.

2

Bioremediation of fluazifop-p-butyl herbicide by some soil bacteria isolated from various regions of Turkey in an artificial agricultural field

Erguven Gokhan Onder, Nuhoglu Yasar

Environment Protection Engineering

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2020

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Vol. 46, nr 3

5--15

EN

The bioremediation rate of fluazifop-p-butyl (C19H20F3NO4) was monitored. Bacteria were isolated in agricultural soil samples. Fifteen sterilised glass jars were inoculated with 2, 5, 10, 20 cm3 of a homogenised bacterial mixture (109 CFU/cm 3), then sterile agricultural soil and 60 μg of fluazifop-p-butyl (in liquid form) were added to each jar. Each week, filtrated water drained from bottles was analysed for fluazifop-p-butyl concentration, chemical oxygen demand (COD), biochemical oxygen demand (BOD5) and total organic carbon (TOC). Additionally, pH and dissolved oxygen concentration were monitored. The highest biodegradation rate was observed in the soil sample containing 20 cm 3 of the culture media. In this media, fluazifop-p-butyl, COD, BOD5 and TOC removals were measured as 91, 83, 96 and 86%, respectively, at the end of the 2 months. The DO level was measured between 3 and 6 mg O2/dm 3 in the first month for all cultures. An increase of pH was recorded during the first month and after this time a pH decrease was noted.

3

Quantitative Analysis of Aerobic Cultivable Bacteria and Soil Total Enzymatic Activity of Kielce and Rudki Urbicenose

Konieczna I., Żarnowiec P., Świercz A., Gruszczyński M., Polkowska-Motrenko H., Chejduk E., Kaca W.

Ecological Chemistry and Engineering. A

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2012

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Vol. 19, nr 8

915-920

EN

The microbiological and biochemical analysis of two urban soil samples, from Swietokrzyskie province (Kielce, Rudki), were performed. The aim of this study was the quantitative analysis of aerobic bacterial microflora and determination of total enzymatic activity of soil from area with high level of street traffic (Kielce) and from former pyrite mine region (Rudki), where uranium ore were extracted. The commercial media (TSA, LB, MacConkey, M9 and King B agars) and soil extract agars were used for soil microorganisms isolation. The bacteria were cultivated in two temperatures: +25 °C and +4 °C. From Kielce urbicenose, amount of soil bacteria cultivated on commercial media were higher in case of culture in +25 °C (from 10 to 108 times more depending on used medium), whereas on soil extract agar almost 2 times more microorganisms were found in +4 °C. For soil contamined by uranium (Rudki), abundant bacterial growth in both temperatures were observed only on soil extract agar. The total ureolytic, proteolytic and lipolytic activities of soil samples were also defined. In case of soil sample from Kielce all from the determinated activities were found, whereas for soil from Rudki only lipolytic activity was noted.

PL

Wykonano badania mikrobiologiczne i biochemiczne dwóch próbek gleb miejskich województwa świętokrzyskiego (Kielce, Rudki). Celem pracy była analiza ilościowa tlenowej hodowalnej mikroflory bakteryjnej oraz określenie całkowitej aktywności enzymatycznej gleby z okolic o dużym natężeniu ruchu drogowego (Kielce) i terenów byłej kopalni pirytu (Rudki), skąd wydobywano rudę uranową. Do izolacji drobnoustrojów zastosowano pożywki komercyjne (TSA, agar LB, MacConkey'a, M9 i King B) oraz podłoża z ekstraktami glebowymi. Hodowlę prowadzono w dwóch temperaturach: +25 °C i +4 °C. W przypadku gleby urbicenozy Kielc, na pożywkach komercyjnych zaobserwowano większą ilość drobnoustrojów hodowanych w temperaturze +25 °C (od 10 do 108 razy więcej w zależności od stosowanej pożywki), natomiast na podłożu z ekstraktem glebowym niemal 2 razy więcej bakterii rosło w temp. +4 °C. W glebie zanieczyszczonej uranem (Rudki) obfity wzrost drobnoustrojów hodowanych w obu temperaturach występował jedynie na agarze z ekstraktem glebowym. Oznaczono również całkowitą aktywność ureolityczną, proteolityczną i lipolityczną próbek glebowych. W przypadku próbek gleby z Kielc obserwowano wszystkie badane aktywności, natomiast dla gleby z Rudek tylko lipolityczną.

4

Characterization of the Aerobic Cultivable Bacteria Isolated from Soils: Heavy Metals Contaminated (Bialogon, Kielce) and Arable (Klonowskie Ridge)

Konieczna I., Żarnowiec P., Świercz A., Kaca W.

Ecological Chemistry and Engineering. A

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2012

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Vol. 19, nr 7

741-747

EN

The aim of this study was quantitative and enzymological analysis of aerobic bacterial microflora isolated from heavy metals contaminated soil and unpolluted arable soil. The amounts of haevy metals: zinc, copper, cadmium, lead, chromium in soil samples were determined. The commercial media and soils extracts media were used for soil microorganisms isolation. Amount of soil bacteria cultivated on commercial media were significant higher (3 to 106 times) in case of heavy metals contaminated soil, whereas during growth on soil extract agar more microorganisms were found in arable soil. The Gram-negative bacteria dominated among strains isolated from both soil samples. For isolated microorganisms the ureolytic and proteolytic activity, as well as the ability for nitrification and denitrification were determined. The total ureolytic and proteolytic activity of soil samples were also defined. It was revealed, that only few bacterial strains isolated from polluted soil indicated analyzed properties (27 % – urea hydrolysis, 13 % – skim milk hydrolysis, 19 % – nitrification and 27 % – denitrification) in comparison with isolates from arable soil (65 %, 35 %, 30 % and 35 % respectively). In heavy metals contaminated soil the total ureolytic activity was much lower than in unpolluted soil sample. The presence of heavy metals has inhibitory effect on appearance of microorganisms participating in nitrogen circulation.

PL

Celem pracy była analiza ilościowa i enzymologiczna tlenowej mikroflory bakteryjnej izolowanej z gleby zanieczyszczonej metalami ciężkimi oraz gleby uprawnej terenów czystych ekologicznie. Próbki zbadano pod względem zawartości metali ciężkich: cynku, miedzi, kadmu, ołowiu, chromu. Do izolacji drobnoustrojów z próbek glebowych zastosowano pożywki komercyjne oraz podłoża z ekstraktami glebowymi. Ilość wyhodowanych mikroorganizmów na pożywkach komercyjnych była znacznie większa (od 3 do 105 razy) w przypadku gleby skażonej metalami ciężkimi, natomiast na podłożu zawierającym ekstrakt glebowy obserwowano bogatszy wzrost bakterii dla gleby uprawnej. Wśród szczepów bakterii wyizolowanych z obu próbek dominowały drobnoustroje Gram-ujemne. Dla wyizolowanych mikroorganizmów określono aktywność ureolityczną, proteolityczną oraz zdolność do przeprowadzania procesów nitryfikacji i denitryfikacji. Oznaczono również całkowitą aktywność ureolityczną i proteolityczną próbek glebowych. Wykazano, że tylko nieliczne szczepy bakterii izolowanych z gleby zdegradowanej wykazywały badane właściwości (27 % - hydroliza mocznika, 13 % - hydroliza białek mleka, 19 % - nitryfikacja i 27 % - denitryfikacja) w porównaniu do izolatów z gleby uprawnej (odpowiednio: 65 %, 35 %, 30 % i 35 %). W glebie zanieczyszczonej metalami ciężkimi całkowita aktywność ureolityczna była znacznie mniejsza w porównaniu do próbki gleby czystej. Obecność metali ciężkich wpływa hamująco na występowanie drobnoustrojów uczestniczących w obiegu azotu.

5

Copper ions as a factor determining the enzymatic activity of soil bacteria

Bałaszak M., Nowak A.

Ecological Chemistry and Engineering. A

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2008

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Vol. 15, nr 1-2

15-21

EN

The experiment bas been aimed at evaluating the war and the range of bacterial activity due to copper ions. Copper(II) chloride dihydrate was introduced into the soil at two rates to achieve the total copper content corresponding to weak and strong soil pollution by the element. After two-month soil incubation several hundreds of bacterial strains were isolated and ranges of proteolytic, amylolytic, and lipolytic activities were determined for every strain. Microorganisms were cultured on solid medium containing casein, tributyrin, or starch. Achieved results were compared with the same activity of microorganisms isolated from control soil. Contamination of soil with copper ions changed bacterial hydrolytic activity to a different degree, but it was not always statistically significant. In most cases, increase in hydrolytically inactive microorganism number and decrease in extremely active strains (from several to several dozens of per cents) was observed after copper chloride application. Higher differences in relation to control were recorded after weak pollution of soil with copper for amylolytic and lipolytic activities.

PL

Celem doświadczenia było ustalenie, czy jony miedzi mogą zmieniać zakres aktywności enzymatycznej populacji bakterii glebowych. Do gleby wprowadzono dihydrat chlorku miedzi(II) w dwóch dawkach, tak by całkowita zawartość miedzi odpowiadała słabemu i silnemu zanieczyszczeniu gleby tym pierwiastkiem. Po dwumiesięcznej inkubacji gleby, izolowano z niej szczepy bakteryjne (po kilkaset) i ustalano zakres ich aktywności proteolitycznej, amylolitycznej i lipolitycznej. Mikroorganizmy hodowano na podłożu stałym z kazeiną, tributyryną lub skrobią. Otrzymane wyniki porównywano do tej samej aktywności mikroorganizmów wyizolowanych z gleby kontrolnej. Zanieczyszczenie gleby jonami miedzi zmieniało w różnym zakresie aktywność hydrolityczną bakterii, jednak nie zawsze w sposób statystycznie istotny. W większości przypadków, po wprowadzeniu do gleby chlorku miedzi, zanotowano zwiększanie się ilości mikroorganizmów nie aktywnych hydrolitycznie oraz zmniejszenie udziału szczepów wybitnie aktywnych (od kilku do kilkudziesięciu procentów). W przypadku aktywności amylolitycznej i lipolitycznej większe różnice wobec kontroli odnotowano po słabym, a nie silnym zanieczyszczeniu gleby miedzią.

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Corrosion and hydrogen damage of steel in contact with soil bacteria and micromices. Preventive ability of organic inhibitors

Beloglazov S.M.

Advances in Materials Science

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2007

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Vol. 7, nr 2(12)

202-209

EN

The martensitic stainless steel (ca. 13%Cr, 2%Ni and 0.25%C) corrodes in anaerobic aqueous salt medium deteriorated with H2S, as metabolic product of sulfate reducing bacteria, with small rate, but absorb a high quantity of hydrogen, that formed a very thin subsurface hydrogen rich layer. It can be explained by existence of collectors in the subsurface of metal, filled withmolecular hydrogen, which prevent the deeper penetration of H while diffusing in steel. Molecularization process of H on the internal collector surface results in growth of partial H2 pressure in collectors. The further diffusion of H into the metal depth then bas to take place through the already stressed and strained metal around the collectors. The stress field prevent the hydrogen diffusion into the depth of steel. The earlier elaborated special steel anodic dissolution technique (step-strip technique) bas been successfully applied for hydrogen analyzing in austenitic steel. The hydrogen concentration profiles gained from these tests may be very useful in the explanation of the hydrogen embrittlement of high-strength Cr-Ni-steels. The H2S-content - time curves in media with SRB have the similar character and sequence as one s SRB cells number (bacterial liter) - time. The OC being studied can act as satisfactory inhibitors of SRB-induced corrosion of martensitic stainless steel in aqueous salt medium. The corrosion inhibiting of OC under study is in a good agreement between their molecular structure and inhibiting efficiency. The increase of electron density on the functional groups provide the made strong adsorption of organic molecules on the steel surface. The bactericidal action of OC on SRB corresponds essentially to their steel corrosion inhibiting effi-ciency in aqueous salt medium. Mould fungi (Aspergillus niger, Penicillium chrysogenum, Penicillium charlissii and Phialophora fastigiata) isolated from soil exhibits stimulating action on steel corrosion visible already after two days of exposure. N-containing OC having linear molecules showed significantly greater inhibiting corrosion action in media with Phialophora fastigiata and Pen. charlissii in comparison with Asp. niger and Pen. chrysogenum.