Saadouli Ilhem, Marasco Ramona, Mejri Lassaad, Hamden Haytham, Guerfali Meriem M'saad, Stathopoulou Panagiota, Daffonchio Daniele, Cherif Ameur, Ouzari Hadda-Imene, Tsiamis George, Mosbah Amor
Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.
Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Front Microbiol. 2022 Dec 13;13:997832. doi: 10.3389/fmicb.2022.997832. eCollection 2022.
Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.
石材表面是一个独特的生物龛位，可能拥有丰富的微生物多样性。探索石材微生物群落的生物多样性既是一项重大挑战，也是一个表征具有宝贵生物活性新菌株的机会。在此，我们通过考虑地理气候区域和石材地球化学的影响，探索了突尼斯罗马石材遗址相关总细菌群落的多样性和适应策略。对从突尼斯三个不同采样点收集的石材样本中提取的DNA进行了环境16S rRNA基因扩增子分析，采样沿着近400公里的干旱梯度进行，涵盖地中海、半干旱和干旱气候。文库在Illumina MiSeq测序平台上进行测序。使用稀释平板技术从石材样本中分离出可培养的放线菌。基于16S rRNA基因序列共分离并鉴定出71株菌株。对可培养放线菌进行了进一步研究，以评估其在石材内外生存所采用的适应策略。扩增子测序表明，石材遗址细菌群落始终以蓝细菌为主，其次是变形菌门和放线菌门，沿干旱梯度分布。然而，细菌群落组成部分的相对丰度根据地理气候来源而变化。石材地球化学，特别是镁、铬和铜的可用性，也影响了细菌群落的多样性。对可培养放线菌进行了进一步研究，以评估其在石材内外生存所采用的适应策略。所有培养的细菌都属于放线菌纲，最丰富的属是链霉菌属、考克氏菌属和节杆菌属。它们能够耐受高温（高达45°C）和盐分积累，并产生参与养分溶解的酶，如磷酸酶、淀粉酶、蛋白酶、几丁质酶和纤维素酶。放线菌成员在细菌之间的共现相互作用中也起着重要作用，有利于群落相互作用组和稳定性。我们的研究结果为放线菌在与石材遗址相关的微生物群落中的多样性、适应性和作用提供了新的见解。
