透過土壤微生物群來了解土壤本身
對全球土壤內部基因體組的首次調查揭露出一場真菌和細菌之間的大戰
by Iris Kruijen
土壤在養分的循環和把碳儲存起來這些方面是不可或缺的；此外，土壤內部也充斥著各式各樣的生命。為了更加了解土壤的功能，由歐洲分子生物學實驗室(EMBL)和愛沙尼亞塔圖爾大學領導的國際研究團隊，對土壤中的細菌和真菌進行了第一起範圍涵蓋全球的研究。他們的結果顯示細菌和真菌為了爭奪養分而衝突不休，並且製造出各式各樣的抗生素兵器來比對方取得更多優勢。這項研究也有助於我們預測氣候變遷對土壤的影響，並讓我們可以更加善用土壤的天然成分來幫助農業發展。研究結果發表於2018年8月1日的期刊《自然》(Nature)。
土壤中的細菌和真菌正在進行一場世界大戰。圖片來源：Falk Hildebrand and Aleksandra Krolik in collaboration with
Campbell Medical Illustration/EMBL
科學家得費盡心力才能進行關於土壤微生物群的研究。在5年的研究過程中，他們從世界各地仔細選出未受人類活動影響(像是農業)的1450個地點，接著從每個地點採集40個土壤樣品，總計多達58000個樣品。第一作者塔圖爾大學 Mohamad Bahram和EMBL的Falk Hildebrand與眾多合作人員共同發起這件龐大的計劃、採集樣品並分析合計多達14.2TB的資料。他們在1450個採樣地點之中選出189個進行更加深入的分析。這189個地點涵蓋了地球各大洲，從熱帶森林至寒帶凍原等全球最重要的生物群系。
在土壤中發生的微生物世界大戰
在此研究中發現的數百萬個基因只有0.5%跟從腸道和海洋微生物群發現的現有數據有所重疊。研究通訊作者，EMBL研究團隊的領導人Peer Bork表示：「這些未知基因的數量令人嘆為觀止。但我們可以解讀的少數基因明確指出土壤裡的細菌和真菌之間正在進行一場世界大戰。」
總括來說，當土壤裡的真菌數量比細菌多的時候，細菌的多樣性也會比較低。此外，研究人員也發現細菌用來產生抗生素抗藥性的基因數量跟真菌的數量之間有很強烈的相關性，特別是跟那些可能會產生抗生素(如盤尼西林)的真菌數量。 Falk
Hildebrand說：「這種模式有個很好的解釋――真菌在對抗細菌的戰事中會製造出抗生素，因此只有含有足夠抗生素抗藥性基因的細菌才能生存下來。」
Mohamad Bahram表示：「細菌和真菌之間的對立狀態影響了細菌群落的整體多樣性，也決定了抗生素抗藥性在基因組庫的多寡。」這項資訊可以用來預測導致抗生素抗藥性的基因在不同生態系中的分布情形，以及這些基因可能會透過什麼路徑傳給人類病原體。此外，這也有助於預測並找出自然界哪裡有可以產生高效抗生素的物種。
區域差異
團隊也發現細菌和真菌的分布情形具有地域上的差異。細菌可謂無所不在，並在溫帶地區的溫和氣候下具有最高的基因多樣性。諸如溫度之類的環境因子在它們的相對數量上具有最為關鍵的影響：細菌通常偏好於濕熱地區；真菌則更加常見於寒原之類的乾冷氣候。此外，它們的分布也很容易受到地理因素的限制，在不同大陸上的族群數目具有差異。這意謂細菌和真菌對養分循環的相對貢獻在世界各地不盡相同，因此氣候變遷對它們組成和功能的影響在各地可能也不一樣。
人類活動的影響
比較土壤未受開發的地點與受到人類活動影響的地點，像是農地或是庭院草坪，數據顯示細菌、真菌和抗生素之間的比例完全不同。自然演化成的平衡狀態或許經歷了地球歷史上的大部分時光。據這些科學家所述，自然平衡的改變顯示人類活動對土壤微生物群的影響會造成目前仍無法得知的後果。不過，更加理解土壤中真菌和細菌之間的交互作用，有助於我們的農業減少土壤肥料的使用，讓具有益處的微生物有更多機會可以在自然環境中存活下來。
Understanding soil through its microbiome
First global survey of soil genomics reveals a war between
fungi and bacteria
Soil is full of life, essential for nutrient cycling and carbon
storage. To better understand how it functions, an international research team
led by EMBL and the University of Tartu (Estonia) conducted the first global
study of bacteria and fungi in soil. Their results show that bacteria and fungi
are in constant competition for nutrients and produce an arsenal of antibiotics
to gain an advantage over one another. The study can also help predict the
impact of climate change on soil, and help us make better use of natural soil
components in agriculture. Nature publishes
the results on 1 August 2018.
Research on the soil
microbiome requires scientists to get their hands dirty. Over the course of
five years, 58.000 soil samples were collected from 1450 sites all over the
world (40 subsamples per site), that were carefully selected to be unaffected
by human activities such as agriculture. First authors Mohamad Bahram
(University of Tartu) and Falk Hildebrand (EMBL), together with a large team of
collaborators, set up this massive project, gathered samples, and analysed the
14.2 terabyte dataset. Of the 1450 sites sampled, 189 were selected for
in-depth analysis, covering the world’s most important biomes, from tropical
forests to tundra, on all continents.
Global microbial war in soil
Only half a
percent of the millions of genes found in this study overlapped with existing
data from gut and ocean microbiomes. “The amount of unknown genes is
overwhelming, but the ones we can interpret clearly point to a
global war between bacteria and fungi in soil,” says Peer Bork, EMBL group
leader and corresponding author of the paper.
Overall, the bacterial
diversity in soil is lower if there are relatively more fungi. The team also
found a strong link between the number of antibiotic resistance genes in
bacteria and the amount of fungi, especially those with potential for
antibiotics production such as Penicillium. Falk Hildebrand: “This pattern
could well be explained by the fact that fungi produce antibiotics in warfare
with bacteria, and only bacteria with adequate
antibiotic resistance genes can survive this.”
“The
antagonism between fungi and bacteria influences the overall diversity of
bacterial communities and determines their genetic repertoire of antibiotic
resistance”, says Mohamad Bahram. This information can be used to predict
the spread of genes that lead to antibiotic resistance in different ecosystems,
and via what routes they may reach human pathogens. It could also help predict
and pinpoint locations with high levels of natural antibiotics producers.
Regional differences
The team also
found regional differences in the distribution of bacteria and fungi. Bacteria
are everywhere, with the highest genetic diversity in temperate zones with a
moderate climate. Environmental factors such as temperature are most decisive
in their relative abundance: they often prefer hot and wet locations. Fungi are
usually more prevalent in colder and dryer climates like the tundra. They also
tend to be more geographically restricted, with differences in populations
between continents. This implies that the relative contributions of bacteria
and fungi to nutrient cycling are different around the world, and that global climate
change may affect their composition and function differently.
Effects of human activity
When comparing
data from the unspoiled soil sites with data from locations affected by humans,
such as farmland or garden lawns, the ratios between bacteria, fungi and
antibiotics were completely different. According to the scientists, this shift
in the natural balance – that probably evolved over most of the earth’s history
– shows the effect of human activities on the soil microbiome, with unknown
consequences so far. However, a better understanding of the interactions
between fungi and bacteria in soil could help to reduce the usage of soil
fertilizer in agriculture, as one could give beneficial microorganisms a better
chance at survival in their natural environment.
原始論文：Mohammad
Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A.
Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis
Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R.
Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi
Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork. Structure and
function of the global topsoil microbiome. Nature, 2018;
DOI: 10.1038/s41586-018-0386-6
引用自：European Molecular Biology Laboratory.
"Understanding soil through its microbiome."
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