Microbial Inheritance in Seeds

Plants are not just plants - rather, a plant is a host to thousands of species of symbiotic bacteria and fungi that reside on its surface and inside its roots, stems and leaves, greatly impacting its overall health and functioning. The plant microbiome plays a fundamental role in a plant's ability to acquire nutrients, resist diseases, and tolerate drought, herbivores and other environmental stresses. Plants are experts at regulating their microbiome, as part of its adaptive responses to environmental conditions. They can pick up new microbes from the environment or break ties with microbial symbionts to increase their chances of survival. For example, associating with a particular species of endophytic fungi can mean the difference between life and death during drought conditions.

Similarly, seeds are not simply packets of plant genes, but also propagules of the plant-symbiotic microorganisms, passing along diverse bacteria and fungi to their offspring. Seedborne "microbial inheritance" allows plant species to maintain beneficial relationships with microbes across plant generations, which is particularly important in agriculture, where the vast majority of our crops are annuals or biennials, dying back every year or so. We can consider the plant microbiome as a more fluid, adaptable form of plant inheritance than plant genetics. The acquired microbial associations that increase the fitness of the plant are the most likely to be passed along in seeds. Thus, seeds are a good place to look for beneficial plant microbes. To make things more complicated, pathogens can 'hitch-hike' across plant generations via the seed. Seed companies often treat their seeds against pathogens as a precaution of spreading disease. But at what cost? What benficial microbes are are we losing by disinfecting seeds against pathogens?

This research project seeks to uncover the hidden world of seedborne microbial inheritance, focusing on open-pollinated corn. How efficient is this form of transmission? How are we affecting microbial inheritance through our farming practices? Can we link desired plant traits (e.g. drought tolerance or disease resistance) to the presence of particular seedborne microbes?

How to participate

The simplest way to participate in this project is to grow and send in open-pollinated corn seeds! We are building a database of seedborne microbes from a growing diversity of corn seed samples - dent, flour, flint, sweet, and popcorn (over 80 samples so far!). We are using cutting-edge DNA sequencing technology to identify the entire population of seedborne bacteria and fungi in each sample. The goal is to look for overall trends between seedborne microbes and corn variety type, traits, and growing practices. If you are looking for a source of seeds, I would recommend growing the Cascade Ruby-Gold flint corn variety from Carol Deppe's Fertile Valley Seeds - Carol is the original breeder. You can also order it from Adaptive Seeds, who is also participating in the project. This particular variety has been most characterized in the project so far, so it will be informative to see how it grows in more locations and farming systems. If you have your own variety that you have been stewarding, that's great too!

Another way to participate is to conduct your own experiments, and send in seed samples from different treatments or selections. For example, perhaps you have been saving seeds of a particular corn variety from plants that do well in low irrigation conditions. You can send in seeds from the better-performing plants, and also seeds from the worse-performing plants, and see how their seedborne microbes are different, to identify candidate beneficial microbes. Another example might be a controlled field experiment where you use a special amendment (say, a microbial inoculant) and are testing how well it performs against a control treatment. You can send in seeds from the control and the treatment, and see how that affected the seedborne microbes. If you decide to go this route, please contact me ([e-mail]) to plan out experiment details.

Sending in your seed samples

A seed sample should represent a particular harvest or selection of seeds from a corn variety that you grew in a single season. Because we are interested in how we affect microbial inheritance through time, we encourage you to also send in samples from any previous years you grew them, and also samples from original seed sources - unless you sourced seeds directly from me or participating seed companies Adaptive Seeds (adaptiveseeds.com) or Carol Deppe’s Fertile Valley Seeds (http://www.caroldeppe.com/Seed%20List%202015.html) because we already have seed microbial data from those sources. Each sample should contain a representative 20-50 seeds. Visit the website for more details (www.microbialinheritance.org/network/seedsample). To receive microbial community data from your seed samples, please fill out the online Seed Sample Submission Form for each seed sample. After filling out the each form, you will receive an email with ID number to include along with your seed sample, in addition to the mailing address where to send the sample.

植物远不止单纯的植物体——实际上，植物是数千种共生细菌与真菌的宿主，这些微生物或附着于植物表面，或定殖于根、茎、叶内部，对植物的整体健康与生理功能有着深远影响。
植物微生物组（plant microbiome）在植物获取养分、抵御病害、耐受干旱、抵御草食动物胁迫及其他环境压力的能力中扮演着核心角色。植物具备调控自身微生物组的能力，这是其适应环境条件的适应性响应的一部分。它们可以从环境中获取新的微生物，也可以切断与微生物共生体的联系以提升生存概率。例如，与特定的内生真菌（endophytic fungi）建立共生关系，可能决定了植物在干旱条件下的生死存亡。

同样，种子也并非单纯的植物基因载体，同时也是植物共生微生物的繁殖体，会将多样的细菌与真菌传递给后代。种子携带的“微生物遗传”（microbial inheritance）使得植物物种能够在多代间维持与微生物的有益共生关系，这在农业领域尤为重要——当前绝大多数作物为一年生或二年生植物，每年都会枯萎死亡。我们可以将植物微生物组视为比植物遗传学更具流动性、适应性的遗传形式。能够提升植物适合度的后天获得的微生物共生关系，最有可能通过种子传递下去。因此，种子是探寻有益植物微生物的优质载体。但情况更为复杂的是，病原体也可通过种子“搭便车”，在植物多代间传播。种子公司通常会对种子进行病原体处理，以预防病害扩散，但这背后付出了何种代价？我们在为抵御病原体而消毒种子的过程中，流失了哪些有益微生物？

本研究项目旨在揭开种子携带微生物遗传的隐秘世界，研究对象为开放授粉玉米（open-pollinated corn）。这种传递方式的效率如何？我们的耕作实践会如何影响微生物遗传？我们能否将目标植物性状（如耐旱性或抗病性）与特定种子携带微生物的存在建立关联？

### 参与方式
最简单的参与方式是种植并寄送开放授粉玉米种子！我们正在搭建涵盖愈发多样的玉米种子样本的种子携带微生物数据库，样本类型包括马齿型（dent）、粉质型（flour）、硬粒型（flint）、甜玉米（sweet）以及爆裂玉米（popcorn）（目前已收集超过80个样本！）。我们采用前沿DNA测序技术，鉴定每个样本中全部的种子携带细菌与真菌群落。研究目标是探寻种子携带微生物与玉米品种类型、性状及种植实践之间的整体关联。

如果你需要种子来源，我们推荐选择卡罗尔·德普（Carol Deppe）的Fertile Valley Seeds中的喀斯喀特红宝石硬粒玉米（Cascade Ruby-Gold flint corn）品种——卡罗尔是该品种的原始育种者。你也可以通过Adaptive Seeds订购，该公司也参与了本项目。截至目前，该品种是本项目中研究最为充分的品种，因此在更多地点和种植系统中开展种植将有助于获取更多有价值的数据。如果你拥有自己长期管护的品种，也同样欢迎参与！

另一种参与方式是开展自主实验，并寄送不同处理或选育条件下的种子样本。例如，你可能一直在保存某一玉米品种的种子，该品种的植株在低灌溉条件下生长良好。你可以分别寄送生长表现优异植株的种子，以及生长表现较差植株的种子，对比二者的种子携带微生物差异，以筛选出潜在的有益微生物。另一个例子是受控田间实验：你使用了特殊的改良剂（如微生物接种剂（microbial inoculant）），并将其与对照组进行效果对比，你可以分别寄送对照组与处理组的种子，观察其对种子携带微生物的影响。如果你选择该路径，请联系我们（[e-mail]）以规划实验细节。

### 寄送种子样本须知
种子样本应代表你在单个生长季种植的某一玉米品种的特定收获或选育的种子。鉴于我们关注的是耕作实践如何随时间影响微生物遗传，我们鼓励你同时寄送过往年份种植的样本，以及原始种子来源的样本——但如果你直接从我司或参与本项目的种子公司Adaptive Seeds（adaptiveseeds.com）或卡罗尔·德普的Fertile Valley Seeds（http://www.caroldeppe.com/Seed%20List%202015.html）获取种子，则无需寄送，因为我们已拥有这些来源的种子微生物数据。每个样本应包含具有代表性的20-50粒种子。更多详情请访问官网（www.microbialinheritance.org/network/seedsample）。

若你希望获取自己寄送的种子样本的微生物群落数据，请为每个种子样本填写在线的“种子样本提交表”。填写完每份表格后，你将收到一封包含唯一编号的邮件，该编号需随种子样本一同寄送，同时邮件中也会包含寄送地址。