Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

根际 基因组 稳定同位素探测 生物 大块土 土壤微生物学 植物 细菌 基因 基因组 计算生物学 遗传学 微生物
作者
Evan Starr,Shaojun Shi,Steven J. Blazewicz,Benjamin J. Koch,Alexander J. Probst,Bruce A. Hungate,Jennifer Pett‐Ridge,Mary K. Firestone,Jillian F. Banfield
出处
期刊:mSphere [American Society for Microbiology]
卷期号:6 (5) 被引量:27
标识
DOI:10.1128/msphere.00085-21
摘要

The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO2-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
赘婿应助beiest采纳,获得10
刚刚
刚刚
又又完成签到,获得积分10
1秒前
鱼清发布了新的文献求助10
1秒前
1147468624完成签到,获得积分20
2秒前
落卿然发布了新的文献求助10
2秒前
生动丑发布了新的文献求助30
2秒前
di123发布了新的文献求助10
3秒前
深情安青应助KYRIELIU采纳,获得10
3秒前
啊伟发布了新的文献求助10
4秒前
wjx发布了新的文献求助10
4秒前
诚心毛巾发布了新的文献求助10
4秒前
无奈完成签到,获得积分10
4秒前
结实的凤妖完成签到,获得积分10
5秒前
姜然完成签到,获得积分10
5秒前
6秒前
6秒前
6秒前
Tinmuse完成签到,获得积分10
6秒前
樱悼柳雪发布了新的文献求助10
7秒前
8秒前
8秒前
9秒前
mhy发布了新的文献求助10
9秒前
金红水晶完成签到,获得积分10
9秒前
小哥格格完成签到 ,获得积分10
11秒前
11秒前
欣喜的秋灵应助风趣飞柏采纳,获得10
11秒前
爱听歌白薇完成签到 ,获得积分20
12秒前
12秒前
万能图书馆应助英吉利25采纳,获得10
12秒前
量子星尘发布了新的文献求助10
13秒前
有你好梦完成签到,获得积分10
13秒前
13秒前
14秒前
千叶伶完成签到,获得积分10
14秒前
彭于晏应助耍酷的小土豆采纳,获得10
14秒前
顾矜应助耍酷的小土豆采纳,获得10
14秒前
stefan发布了新的文献求助10
14秒前
英姑应助di123采纳,获得10
14秒前
高分求助中
Picture Books with Same-sex Parented Families: Unintentional Censorship 700
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
Nucleophilic substitution in azasydnone-modified dinitroanisoles 500
不知道标题是什么 500
Indomethacinのヒトにおける経皮吸収 400
Phylogenetic study of the order Polydesmida (Myriapoda: Diplopoda) 370
Effective Learning and Mental Wellbeing 300
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3974844
求助须知:如何正确求助?哪些是违规求助? 3519270
关于积分的说明 11197844
捐赠科研通 3255496
什么是DOI,文献DOI怎么找? 1797791
邀请新用户注册赠送积分活动 877187
科研通“疑难数据库(出版商)”最低求助积分说明 806202