Diversity of prokaryotic communities of some substrates from sulfide karst caves of the Chechen Republic

Abstract

A comprehensive study of prokaryotic communities (microbiomes) of bacterial mats and snottites from the karst cave Sheki-Kh’ekh was carried out for the first time, with comparison to cave soil-like bodies (SLBs) from the Muhammed-Kh’ekh cave and adjacent brown forest soil. The total abundance of bacterial cells in mats and snottites varied within a relatively narrow range, from 0.26 to 0.35 billion cells per mL, reaching maximum values in floating bacterial mats and minimum values in snottites. In soil-like bodies, the total bacterial abundance was 0.28 billion cells per g. Actinomycete mycelium was detected in all cave samples, with the highest values observed in floating bacterial mats and the lowest in shoreline bacterial mats.
Metabarcoding analysis (16S rRNA gene sequencing) revealed high taxonomic diversity of prokaryotic communities across the studied substrates. The greatest diversity was recorded in floating bacterial mats (25 phyla and 74 genera). In all cave substrates, the dominant phyla were Pseudomonadota and Bacillota, while Bacteroidota also dominated in floating bacterial mats. Lower relative abundances were observed for Actinomycetota, Verrucomicrobiota, Chloroflexota, Chlorobiota, and Thermodesulfobacteriota. Eleven bacterial phyla were shared between soil and floating bacterial mats: Pseudomonadota,Bacillota,Bacteroidota,Verrucomicrobiota,Chlorobiota,Chloroflexota,Actinomycetota,Acidobacteriota,Cyanobacteriota,Planctomycetota, and Armatimonadota, along with two candidate phyla, Sumerlaeota and Hydrogenedentes. Two archaeal phyla, Woesearchaeota and Nanoarchaeota, were detected in bacterial mats.
A total of 191 bacterial genera were identified across all studied substrates. Only 12 genera were common to bacterial mats and soil: Brevundimonas,Devosia, Flavobacterium,Luteolibacter, Paenibacillus,Paenisporosarcina,Pseudarthrobacter, Pseudomonas,Rhodanobacter,Sphingomonas, Sumerlaea, and Thermomonas. A distinctive feature of floating bacterial mat communities was the high representation of genera involved in sulfur cycling processes. Functional profiling revealed the predominance of sulfur- and iron-cycle-related functions in bacterial mats, whereas nitrogen-cycle-related functions and chemoheterotrophy prevailed in soil communities.
This study significantly expands current knowledge of the taxonomic composition of prokaryotic communities inhabiting bacterial mats and snottites of sulfidic caves in the Chechen Republic. The presence of bacterial genera involved in sulfur and iron transformation processes highlights their ecological significance. The results obtained on the diversity of prokaryotic communities in mats, snottites, and soil-like bodies are of interest for understanding ecosystem functioning and for the targeted search of strains with valuable biotechnological properties.

References

1.    Белов А.А., Чепцов В.С., Лысак Л.В. Методы идентификации почвенных микроорганизмов. М., 2020.
2.    Горячкин С.В. География экстремальных почв и почвоподобных систем // Вестн. Рос. акад. наук. 2022. Т. 92, № 6. С. 564–571. https://doi.org/10.31857/S0869587322060056
3.    Горячкин С.В., Мергелов Н.С., Таргульян В.О. Генезис и география почв экстремальных условий: элементы теории и методические подходы // Почвоведение. 2019. № 1. С. 5–19. https://doi.org/10.1134/S0032180X19010040
4.    Джабраилов С.-Э.М., Самохин Г.В. Перспективы развития спелеотуризма в Чеченской Республике // Вестн. КНИИ РАН. 2020. № 1(1). С. 156–177. https://doi.org/10.34824/VKNIIRAN.2020.62.61.021
5.    Звягинцев Д.Г. Методы почвенной микробиологии и биохимии. М., 1991. 304 с.
6.    Лысак Л.В., Добровольская Т.Г., Скворцова И.Н. Методы оценки бактериального разнообразия почв и идентификации почвенных бактерий. М., 2003. 120 с.
7.    Мазина С.Е., Карпова М.С., Голубничая М.А. и др. Микробиота глинистых отложений пещеры Киндерлинская // Успехи медицинской микологии. 2014. Т. 12, Гл. 2. С. 124–125.
8.    Потапов С.С., ЧервяцоваО.Я., Паршина Н.В. и др. К минералогии пещеры Шеки-Хьех (Шатойский район, Чеченская Республика) // Минералогия техногенеза. 2017. № 18. С. 17–32.
9.    Рябова А.С., Кузьмина Л.Ю., ГалимзяноваН.Ф. Микробные сообщества карстовых пещер // Биология, биохимия, генетика. 2022. № 4. С. 18–25.
10.    Семиколенных А.А.Почвоподобные тела автохемолитотрофных экосистем пещер (на примере пещер хребта Кугитангтау, Восточный Туркменистан): Автореф. дис. … канд. биол. наук. М., 2006.
11.    Теория и практика химического анализа почв / Под ред. Л.А. Воробьевой. М., 2006. 400 с.
12.    Хмурчик В.Т., Максимович Н.Г., Мещерякова О.Ю. Микроорганизмы, карст, нефть и спелеогенез // Пещеры. 2010. Т. 33. С. 130–135.
13.    Abraham W.R., Rohde M., Bennasar A. The family Caulobacteraceae // The Prokaryotes: Alphaproteobacteria and Betaproteobacteria / Eds. E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, F. Thompson, 2022. P. 901–918. https://doi.org/10.1007/978-3-642-30197-1_259
14.    Bray J.R., Curtis J.T. An ordination of the upland forest communities of southern Wisconsin // Ecol. Monogr. 1956. Vol. 26, № 4. P. 325–349.
15.    Canaveras J.C., Sanchez-Moral S., Soler V., Saiz-Jimenez C. Microorganisms and microbially induced fabrics in cave walls // Geomicrobiol J. 2001. Vol. 18. P. 223–240.
16.    Chervyatsova O.Y., Potapov S.S., Kuzmina L.Y. et al. Sulfuric acid speleogenesis in the North Caucasus: Sharo-Argun valley Caves (Chechen Republic, Russia) // Geomorphology. 2020. Vol. 369. P. 107346.https://doi.org/10.1016/j.geomorph.2020.107346
17.    De Waele J., D’Angeli I.M., Audra P. et al.Sulfuric acid caves of the world: A review // Earth-Sci. Rev. 2024. Vol. 250. P. 104693. https://doi.org/10.1016/j.earscirev.2024
18.    Forti P. The role of the sulfide–sulfate reaction in the speleogenesis // Proc. 1st Congr. FEALC. OuroPreto (Brazil), 1988. P. 71–73.
19.    Hose L.D., Pisarowicz J.A. Cueva de Villa Luz, Tabasco, Mexico: reconnaissance study of an active sulfur spring cave and ecosystem // J. Cave Karst Stud. 1999. Vol. 61, № 1. P. 13–21.
20.    Jones D., Albrecht H., Dawson K. et al. Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm // ISME J. 2012. Vol. 6. P. 158–170. https://doi.org/10.1038/ismej.2011.75
21.    Jones D.S., Northup D.E. Cave decorating with microbes: geomicrobiology of caves // Elements. 2021. Vol. 17. P. 107–112. https://doi.org/10.2138/gselements.17.2.107
22.    Louca S., Wegener Parfrey L., Doebeli M. Decoupling function and taxonomy in the global ocean microbiome // Science. 2016. Vol. 353. P. 1272–1277. https://doi.org/10.1126/science.aaf4507
23.    Magurran A.E. Measuring biological diversity. Oxford, 2013. 264 p.
24.    Pruesse E., Quast C., Knittel K. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB // Nucleic Acids Res. 2007. Vol. 35. P. 7188–7196. https://doi.org/10.1093/nar/gkm864
25.    Reboleira A.S., Bodawatta K.H., Ravn N.M.R. et al. Nutrient-limited subarctic caves harbour more diverse and complex bacterial communities than their surface soil // Environ. Microbiome. 2022. Vol. 17. art. 41. https://doi.org/10.1186/s40793-022-00435-z
26.    Riquelme C., Hathaway J.J.M., Dapkevicius M.L.E. et al. Bacterial communities in sulfurous caves: diversity, structure and functional potential // Front. Microbiol. 2015. Vol. 6. P. 484. https://doi.org/10.3389/fmicb.2015.01342
27.    Sarbu S.M., Aerts J.W., Flot J.-F. et al. Sulfur Cave (Romania), an extreme environment with microbial mats in a CO₂–H₂S/O₂ gas chemocline dominated by mycobacteria // Int. J. Speleol. 2018. Vol. 47. P. 173–187. https://doi.org/10.5038/1827-806X.47.2.2164
28.    Tomczyk-Żak K., Zielenkiewicz U. Microbial diversity in caves // Geomicrobiol. J. 2016. Vol. 33, № 1. P. 20–38.
29.    Turrini P., Chebbi A., Riggio F.P. et al. The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives // Front. Microbiol. 2024. Vol. 15. 1370520. https://doi.org/10.3389/fmicb.2024.1370520
30.    Zada S., Xie J., Yang M. et al. Composition and functional profiles of microbial communities in two geochemically and mineralogically different caves // Appl. Microbiol. Biotechnol. 2021. Vol. 105, № 23. P. 8921–8936. https://doi.org/10.1007/s00253-021-11658-4
31.    Zhu Hai-Zhen, Jiang Cheng-Ying, Liu Shuang-Jiang. Microbial roles in cave biogeochemical cycling // Front. Microbiol. 2022. Vol. 13. https://doi.org/10.3389/fmicb.2022.950005