Struktura mikrobne združbe v jami Dupnisa, Kırklareli, Turčija

Stabilna temperatura, tema, velika zračna vlaga in omejena količina organske snovi so dejavniki, ki jamski ekosistem opredelijo kot ekstremno okolje in mu dajejo velik pomen v mikrobioloških študijah. Čeprav so bili izsledki študij z gojitvenimi metodami v jamah podobni izsledkom, pridobljenim z molekularnimi metodami, so zadnjenavedene omogočile določitev pestrejšega nabora mikroorganizmov. Spremenljivost mikroorganizmov se razlikuje glede na značilnosti posamezne jame. Cilj te študije je opredeliti raznovrstnost mikrobov v vzorcih iz petih predelov (vključno s turističnim predelom) jame Dupnisa in odkriti razlike med temi predeli. To je prva mikrobiološka študija jamskih sedimentov iz jamskega sistema Dupnisa na SZ Turčije. S sekvenciranjem Illumina Miseq naslednje generacije je bilo 14 debel in 298 rodov pripisanih bakterijskim OTU, 2 debli in 20 rodov pa arhejskim OTU. V bakterijski združbi prevladujejo debla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi in Acidobacteria, združbo arhej pa zastopata debli Thaumarchaeota in Euryarchaeota. Med bakterijami je vodilno deblo Proteobacteria, pri arhejah pa Thaumarchaeota. Indeks pestrosti Chao1 kaže na največjo pestrost bakterij na vzorčnem mestu AF (vhod v jamo/sediment), največjo pestrost arhej pa na vzorčnem mestu F2 (turistični del 2/jamski sediment). Glede na Shannon-Wienerjev indeks pestrosti je bila največja raznolikost rodov arhej in bakterij na vzorčnem mestu F2.Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index

Pregled bakterij v vrtači Yarık, Antalja, Turčija, v zvezi z raztapljanjem karbonata, biomineralizacijo in biotehnološkim potenciali

Abiotic and biotic factors, especially microorganisms, play a role in the development of cave formations and the existence of unique characteristics of each cave. Due to the ecological conditions that characterize the cave environments, highly specialized microorganisms that are the main source of diverse bioactive compounds, inhabit these environments. The aim of this study is to determine the role and biotechnological potential of the bacteria isolated from Yarık Sinkhole located in Antalya (Turkey) by screening their ability to induce the CaCO3 precipitation, to hydrolyze urea, to induce calcite dissolution, and screening their possession of NRPS/PKS gene clusters. The most prevalent phylum is the Bacillota (synonym Firmicutes) (75.7 %), while the dominant species is Bacillus pumilus (33 %). All the isolates showed crystal formation on B4 agar medium, and the Energy dispersive X-Ray spectroscopy (EDS) analyses showed that the crystals are predominately composed of calcium, carbon and oxygen. Ninety-six (96 %) of our isolates have negative ureolytic activity. According to this result and having the ability to induce the CaCO3 precipitation, bac­teria in this environment use other biosynthesis pathways than urea hydrolysis. MgCO3 and CaCO3 were dissolved by 61 % and 59 % of the isolates, respectively. In addition, 5.9 % and 53.7 % of the isolates showed the possession of PKS and NRPS genes, respectively. This result reveals that our isolates have high in­dustrial and biotechnological potential. They may constitute good candidates for further biotechnological applications such as construction of bio-concretes, bioremediation, soil fertility, and production of biologically active secondary metabolites.Abiotski in biotski dejavniki, zlasti mikroorganizmi, imajo pomembno vlogo pri nastanku jamskih oblik in glede edinstvenih značilnosti vsake jame. Zaradi ekoloških razmer, ki so značilne za jamska okolja, ta okolja naseljujejo visoko specializirani mikroorganizmi, ki so glavni vir raznih bioaktivnih spojin. Cilj te študije je opredeliti vlogo in biotehnološki potencial bakterij, izoliranih iz vrtače Yarık v Antalji (Turčija), s pregledom njihove zmožnosti, da povzročijo obarjanje CaCO3, hidrolizirajo sečnino, povzročijo raztapljanja kalcita, in njihove vsebnosti genskih skupin NRPS in PKS. Najpogostejše deblo je Bacillota (sinonim: Firmicutes) (75,7 %), prevladujoča vrsta pa je Bacillus pumilus (33 %). Pri vseh izolatih se je na agarnem gojišču B4 pojavila tvorba kristalov, analize z energijsko disperzivno rentgensko spektroskopijo (EDS) pa so pokazale, da so kristali sestavljeni pretežno iz kalcija, ogljika in kisika. Šestindevetdeset (96 %) naših izolatov ima negativno ureolitično aktivnost. Glede na ta rezultat in zmožnost, da povzročijo obarjanje CaCO3, bakterije v tem okolju upora­bljajo druge načine biosinteze, ne hidrolizo sečnine. MgCO3 in CaCO3 je raztopilo 61 % oziroma 59 % izolatov. Poleg tega je 5,9 % in 53,7 % izolatov imelo gene genskih skupin PKS ozi­roma NRPS. Ta rezultat kaže, da imajo naši izolati velik indus­trijski in biotehnološki potencial. Lahko so zelo primerni za nadaljnjo biotehnološko uporabo, na primer za pripravo bio­betona, bioremediacijo, rodovitnost tal in proizvodnja biološko aktivnih sekundarnih metabolitov

Screening of bacteria in Yarık Sinkhole, Antalya, Turkey for carbonate dissolution, biomineralization and biotechnological potentials

Abiotic and biotic factors, especially microorganisms, play a role in the development of cave formations and the existence of unique characteristics of each cave. Due to the ecological conditions that characterize the cave environments, highly specialized microorganisms that are the main source of diverse bioactive compounds, inhabit these environments. The aim of this study is to determine the role and biotechnological potential of the bacteria isolated from Yarık Sinkhole located in Antalya (Turkey) by screening their ability to induce the CaCO3 precipitation, to hydrolyze urea, to induce calcite dissolution, and screening their possession of NRPS/PKS gene clusters. The most prevalent phylum is the Bacillota (synonym Firmicutes) (75.7 %), while the dominant species is Bacillus pumilus (33 %). All the isolates showed crystal formation on B4 agar medium, and the Energy dispersive X-Ray spectroscopy (EDS) analyses showed that the crystals are predominately composed of calcium, carbon and oxygen. Ninety-six (96 %) of our isolates have negative ureolytic activity. According to this result and having the ability to induce the CaCO3 precipitation, bac­teria in this environment use other biosynthesis pathways than urea hydrolysis. MgCO3 and CaCO3 were dissolved by 61 % and 59 % of the isolates, respectively. In addition, 5.9 % and 53.7 % of the isolates showed the possession of PKS and NRPS genes, respectively. This result reveals that our isolates have high in­dustrial and biotechnological potential. They may constitute good candidates for further biotechnological applications such as construction of bio-concretes, bioremediation, soil fertility, and production of biologically active secondary metabolites

Microbial corrosion and prevention in industrial systems

Mikrobiyolojik korozyon (MIC) mikroorganizmalar tarafından oluşturulan korozyon sürecidir. MIC organik ve inorganik asitler ile metallerin bozunmasına neden olur ve bu yüzden endüstriyel ve diğer sistemlerin yapı bütünlüğünü tehlikeye atarak dünya çapında önemli bir sorun yaratır. Metalik yapıların yüzeyinde meydana gelen kompleks biyolojik ve inorganik süreçlerin doğru bir şekilde anlaşılması MIC’un önlenmesi ve koruma için etkili uygulamalar gerçekleştirmek için gereklidir. Ayrıca bu durum onarım maliyetlerini en aza indirmek için uygun bir strateji geliştirmemize yardımcı olacaktır. Bu derleme endüstriyel sistemlerde kullanılan metal yüzeylerde biyofilm oluşumu, mikrobiyolojik korozyon ve buna neden olan mikroorganizmaların tanımlanması ve sistemlerdeki bu oluşumların engellenmesi için doğru stratejilerin nasıl belirlenebileceğine dair öneriler içermektedir.Microbial corrosion (MIC) is corrosion process enhanced by microorganism. MIC causes deterioration of metals by organic and inorganic acids and thus compromise the integrity of industrial and other systems structures, creating significant problems worldwide. A proper understanding of the complex biological and inorganic processes occurring at the surface of metallic structures is needed to carry out effective treatments for MIC prevention and protection. Besides this situation will help us develop an appropriate strategy to minimize the costs in repairs. This review contains biofilm formation on metal surface used in industrial systems, microbial corrosion and identification of microorganisms that cause it, and in the systems for the prevention of the formation with suggestions for how to determine the right strategy