Alexa K. Byers, Nick Waipara, Leo Condron, Amanda Black
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To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. 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引用次数: 0
摘要
新西兰奥特亚罗瓦以古老的金丝楠木(Agathis australis)为主的森林正受到多种生态干扰的威胁,如森林破碎化、生物多样性丧失、气候变化以及剧毒土壤病原体 Phytophthora agathidicida 的传播。我们的研究从更广泛的生态系统层面入手,旨在探索森林干扰和疾病爆发对凯瑞土壤微生物组的生物合成潜力和分类多样性的影响。我们探索了一系列考瑞森林土壤中次级代谢物生物合成基因簇(BGCs)的多样性,这些土壤因历史干扰和枯死表现而异。为了描述微生物 BGCs 的多样性,我们利用长线程 PacBio® HiFi 测序技术对非核糖体肽合成酶(NRPS)和多酮肽合成酶(PKS)基因区域进行了测序。此外,我们还利用 16 S rRNA 和 ITS 基因区测序鉴定了每片森林的土壤细菌和真菌群落。我们在猕猴桃林土壤中发现了多种多样的天然微生物 BGCs,这些 BGCs 可为探索对 P. agathidicida 具有抗微生物活性的次生代谢物提供有前景的目标。我们发现,不同的森林干扰历史导致微生物 BGCs 的数量和多样性存在差异。值得注意的是,与未受干扰的考瑞森林相关的土壤中,微生物 NRPS 型 BGCs 的数量和多样性较高,这可能是微生物组抵抗病原体入侵的自然水平的一个潜在指标。通过将微生物生物合成多样性的模式与森林干扰历史联系起来,这项研究强调了我们需要考虑生态干扰的影响,因为生态干扰会影响森林土壤生态系统更广泛的健康,从而使森林更容易受到疾病的侵袭。此外,这项研究还确定了高丰度存在于考瑞木土壤中的微生物BGCs的范围,有助于未来发现可能会增强考瑞木林抗病能力的天然微生物化合物。本研究采用的方法强调了在研究微生物群落对生态系统干扰的反应时超越分类学视角的价值,以及开发微生物群落对入侵植物病原体复原力的更多功能测量方法的必要性。
The impacts of ecological disturbances on the diversity of biosynthetic gene clusters in kauri (Agathis australis) soil
The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.
期刊介绍:
Microorganisms, omnipresent across Earth's diverse environments, play a crucial role in adapting to external changes, influencing Earth's systems and cycles, and contributing significantly to agricultural practices. Through applied microbiology, they offer solutions to various everyday needs. Environmental Microbiome recognizes the universal presence and significance of microorganisms, inviting submissions that explore the diverse facets of environmental and applied microbiological research.