Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times

Abstract

Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.

Characterization of gut microbial and metabolite alterations in faeces of Goto Kakizaki rats using metagenomic and untargeted metabolomic approach

“…Total DNA was extracted from 1 g of faeces using a kit (Omega Bio-Tek, Norcross, GA, United States), and the concentration, purity and quality of the DNA was determined[ 15 ].…”

Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms

“…Worldwide, most lithic artifacts have suffered irreversible biodegradation (Abdel Ghany et al, 2019;Trovão et al, 2019;Gambino et al, 2021;Zhang et al, 2021), for example, the Angkor sandstone monuments (Liu et al, 2018), the limestone walls of the old cathedral of Coimbra (Trovão et al, 2019), the Chaalis abbey (Mihajlovski et al, 2017), and the Feilaifeng limestone statue (Li et al, 2018). Southwest China is a typical carbonate area (Chen et al, 2022), where politics, economics, and culture are all linked to carbonate rocks. For example, policies in Southwest China are linked to the ecological restoration of areas exhibiting karstic desertification, and most building materials are limestone.…”

“…Compared to microorganisms in other environments, lithobiontic microorganisms are characterized by (1) low taxonomic diversity but high synergistic and metabolic activity (Villa et al, 2015); (2) phylogenetic similarity and high specificity worldwide (Gorbushina and Broughton, 2009); and (3) pigments, exopolymeric substances, and efficient DNA repair systems that allow survival on the rock (Gómez-Silva, 2018). Rock surface pH, porosity, permeability, mineral composition, texture, geometry, shading, and timing of colonization affect the composition and structure of lithobiontic microbial communities (Miller et al, 2012;Brewer and Fierer, 2018;Liu et al, 2018Liu et al, , 2020Abdel Ghany et al, 2019;Chen et al, 2022). A decrease in rock surface pH is generally regarded as more serious biodeterioration (Pinheiro et al, 2019).…”

“…Limestone is one of the rock types that are more susceptible to biodeterioration. Softness, brightness, and easy sculptability increase the bioreceptivity of limestone (Miller et al, 2012;Pinheiro et al, 2019;Chen et al, 2022). The inorganic compounds in limestone are good substrates for the growth of various microorganisms, with microorganisms obtaining the required elements by secreting organic acids (Warscheid et al, 1991).…”

“…can secrete sulfuric acid, thereby obtaining the necessary chemoenergetic nutrients (Warscheid and Braams, 2000). Our previous study reported on the microbial taxa (and their functional genetic variations) on carbonate rock under natural conditions with various weathering times (Chen et al, 2022). However, it is not clear which microorganisms take the lead in colonizing limestone under natural conditions, or whether acid erosion or nutrient availability promote microbial colonization.…”