Information

1.2D: Environmental Diversity of Microbes - Biology


Learning Objectives

  • Summarize how microbial diversity contributes to microbial occupation of diverse geographical niches.

The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea, and most lineages of the Eukarya are microorganisms. Microbes live in every kind of habitat (terrestrial, aquatic, atmospheric, or living host) and their presence invariably affects the environment in which they grow. Their diversity enables them to thrive in extremely cold or extremely hot environments. Their diversity also makes them tolerant of many other conditions, such as limited water availability, high salt content, and low oxygen levels.

Not every microbe can survive in all habitats, though. Each type of microbe has evolved to live within a narrow range of conditions. Although the vast majority of microbial diversity remains undetermined, it is globally understood that the effects of microorganisms on their environment can be beneficial. The beneficial effects of microbes derive from their metabolic activities in the environment, their associations with plants and animals, and from their use in food production and biotechnological processes.

In turn, the environment and the recent temperature anomalies play a crucial role in driving changes to the microbial communities. For instance, the assemblage of microbes that exists on the surface of seawater is thought to have undergone tremendous change with respect to composition, abundance, diversity, and virulence as a result of climate-driving sea surface warming.

For microbiologists, it is critical to study microbial adaptation to different environments and their function in those environments to understand global microbial diversity, ecology, and evolution. They rely on specific physical and chemical factors such as measuring temperature, pH, and salinity within a certain geography to formulate a comparison among microbial communities and the environment different species can tolerate. Researchers collect samples from geographical areas with different environmental conditions and between seasons to determine how dispersal patterns shape microbial communities and understand why organisms live where they do. As such, microbial communities from coastal and open oceans, polar regions, rivers, lakes, soils, atmosphere, and the human body can be tested. These samplings create a starting point to understand how the abundance and composition of microbial communities correlate with climatic perturbations, interact to effect ecosystem processes, and influence human health. Interfering with natural microbial biomass disrupts the balance of nature and the ecosystem and leads to loss of biodiversity.

Key Points

  • Different microbial species thrive under different environmental conditions.
  • Microbial communities occupy aquatic and terrestrial habitats and constitute the majority of biodiversity on Earth.
  • Microbial diversities sustain the ecosystem in which they grow.

Key Terms

  • biodiversity: The diversity (number and variety of species) of plant and animal life within a region.
  • biomass: The total mass of all living things within a specific area or habitat.

Environmental Microbiology

Molecular biology has revolutionized the study of microorganisms in the environment and improved our understanding of the composition, phylogeny, and physiology of microbial communities. The current molecular toolbox encompasses a range of DNA-based technologies and new methods for the study of RNA and proteins extracted from environmental samples. Currently there is a major emphasis on the application of "omics" approaches to determine the identities and functions of microbes inhabiting different environments.

Microbial life is amazingly diverse and microorganisms literally cover the planet. It is estimated that we know fewer than 1% of the microbial species on Earth. Microorganisms can survive in some of the most extreme environments on the planet and some can survive high temperatures, often above 100°C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly salt|saline, acidic, or alkaline water.

An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species. Microorganisms have special impact on the whole biosphere. They are the backbone of ecosystems of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. So, microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance in the sense that their symbiotic relationship (either positive or negative) have special effects on the ecosystem.

Microorganisms are cost effective agents for in-situ remediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites are typically comprised of multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species/strains, each specific to the degradation of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacterial consortium in order to evaluate the activity level of the bacteria, and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.

Oil Biodegradation
Petroleum oil is toxic and pollution of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult, however much of the oil can be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remediate the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastics and biocatalysis.

Degradation of Aromatic Compounds by Acinetobacter
Acinetobacter strains isolated from the environment are capable of the degradation of a wide range of aromatic compounds. The predominant route for the final stages of assimilation to central metabolites is through catechol or protocatechuate (3,4-dihydroxybenzoate) and the beta-ketoadipate pathway, and the diversity within the genus lies in the channelling of growth substrates, most of which are natural products of plant origin, into this pathway.

Analysis of Waste Biotreatment
Biotreatment, the processing of wastes using living organisms, is an environmentally friendly alternative to other options. Bioreactors have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.

Environmental Genomics of Cyanobacteria
The application of molecular biology and genomics to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting, and functional interrogation of natural populations have become common, enabled by a battery of molecular and bioinformatics techniques. Recent studies on the ecology of Cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological, and geochemical techniques have combined in the study of natural communities of these bacteria.


Researchers find maintenance mechanism of microbial diversity in Tibet wetlands

Abundant bacteria and fungi exhibit broader environmental breadths and stronger phylogenetic signals of ecological preference than corresponding rare ones. Rare microbial taxa show closer phylogenetic clustering than abundant microbial taxa. Soil ammonia is the decisive factor in shaping the balance between community assembly processes of rare and abundant microbial taxa, showing distinct changes in stochasticity with higher ammonia content. Credit: WBG

Microorganisms participate in biogeochemical cycles of key elements (e.g., carbon, nitrogen, phosphorus, and sulfate), and their diversity is closely correlated with soil ecosystem functions. Disentangling the geographic distribution pattern and microbial diversity maintenance mechanism is of significance to estimate diversity-driven ecosystem functions and potentials. However, study on the maintenance mechanism of microbial diversity in the wetland ecosystems is poorly understood.

Associate professor Wan Wenjie, professor Yang Yuyi and professor Liu Wenzhi from Wuhan Botanical Garden, collaborated with professor Geoffrey Michael Gadd of the Dundee University in UK and professor GU Jidong of the Hong Kong University, took Qinghai-Tibet Plateau as the research object, and determined community composition and diversity of both bacteria and fungi along with environmental gradient.

The researchers employed multiple statistical analysis approaches to calculate environmental breadths, phylogenetic signals, phylogenetic clustering, and ecological community assembly processes.

Abundant bacterial and fungal subcommunities show broader environmental breadths and stronger phylogenetic signals of ecological preference than corresponding rare bacterial and fungal subcommunities. On the contrary, rare microbial subcommunities exhibit closer phylogenetic clustering than abundant microbial subcommunities.

In addition, deterministic processes dominate in the rare bacterial subcommunity, while stochastic processes govern abundant bacterial subcommunity, and rare and abundant fungal subcommunities.

The variation partitioning analysis and neutral model analysis further validates that abundant taxa are less environmentally constrained. Soil ammonia is crucial for shaping the balance between community assembly processes of rare and abundant microorganisms, showing distinct changes in stochasticity with higer ammonia content.

These findings provide new insights and statistical methods for assessing the maintenance mechanism of microbial diversity in wetland ecosystems, and enriches the theoretical basis for the environmental protection of wetland ecosystems in Qinghai-Tibet Plateau.

The research was funded by the National Natural Science Foundation of China, Youth Innovation Promotion Association of Chinese Academy of Sciences, and National Science & Technology Fundamental Resources Investigation Program of China. The findings have been published in the SCI Journal of Molecular Ecology, titled "Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau."


Introduction

Many multicellular organisms harbor dense microbial communities that are vital for host health providing nutrients, protecting from pathogens, and promoting immune system development [1–4]. However, most hosts are not born with these diverse communities. Instead, their microbiomes gradually assemble after birth, progressing over time from a state of low diversity to form richer multispecies communities [5–8]. In many hosts, this developmental process is remarkably predictable, with the same characteristic taxa colonizing the gut at different points during development in most individuals [5–9]. And, crucially, the ordered nature of this acquisition of a diverse microbiome community is often considered critical for health. In corals, for example, symbionts that are beneficial to adults can be detrimental if acquired too early in development [10]. Meanwhile, in humans, failure to establish a stable and diverse microbiome is associated with numerous pathologies, including necrotizing enterocolitis, a devastating disease that causes significant morbidity and mortality in premature infants [11,12]. However, despite this importance, we still understand little about what causes a given microbiome community to assemble and persist.

While there is a large and rapidly growing body of empirical data on host-associated microbiomes [13], it remains challenging to disentangle the drivers of microbiome assembly, because so many species and processes can be potentially conflated. However, there is a long history in ecology—and many other areas, from weather prediction to neurobiology—of developing complementary theory to understand such complex systems. The great power of these methods is the ability to model vast numbers of different scenarios and thereby identify general principles that can elude empirical work alone. In this tradition, here we develop a theoretical framework to investigate potential drivers of microbiome community assembly.

We extend ecological network theory to ask, for any given community, what are the possible pathways by which it might assemble from an uncolonized environment. Our work suggests that diverse microbiome communities can most robustly assemble when the constituent species interact with one another weakly and in a predominantly noncooperative manner. When hosts rely on strong metabolic interactions within their microbiome, therefore, they face a problem as these interactions can limit community assembly. However, our theory also suggests that when they do occur, strong positive interactions may play a key role in increasing the predictability of community assembly. We also identify interventions that hosts can perform to overcome barriers to assembly, via selecting for ecologically dependent species, or promoting their co-colonization with partner species. Our models provide a framework with which to predict how an array of host-mediated and microbial interactions may affect the assembly process in any host–microbe system, and we illustrate this by supporting our key results with recently published data.


Basic knowledge of biology equivalent to the junior high school level

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About this course

Life on our planet is diverse. While we can easily recognize this in our everyday surroundings, an even more diverse world of life can be seen when we look under a microscope. This is the world of microorganisms. Microorganisms are everywhere, and although some are notorious for their roles in human disease, many play important roles in sustaining our global environment. Among the wide variety of microorganisms, here we will explore those that thrive in the most extreme environments, the extremophiles.

In this course, we will discover how diverse life is on our planet and consider the basic principles that govern evolution. We will also learn how we can classify organisms. Following this, we will have a look at several examples of extreme environments, and introduce the microorganisms that thrive under these harsh conditions. We will lay emphasis on the thermophiles, extremophiles that grow at high temperatures and will study how proteins from thermophiles can maintain their structure and function at high temperatures.


Earth Microbiology Initiative

Microorganisms fill essential functional roles in all of Earth&rsquos ecosystems yet our understanding of microbial abundance, distribution, and metabolism remains surprisingly limited. Columbia University&rsquos new Earth Microbiology Initiative (EMI) has brought together a group of scientists and engineers from across the University to begin coordinated research on Earth&rsquos microbial life. The Earth Microbiology Initiative leverages existing disciplinary resources into broad and interdisciplinary analyses of the extent and diversity of microbial life, its role in maintaining Earth&rsquos living system, and its interactions with natural and human-induced variations.

Recent technological advances provide many new and exciting opportunities to study microorganisms and have begun to reveal information that revolutionizes our view of the natural world and its functioning. Microbes have effectively colonized nearly every imaginable environment including the human body, our backyards, the deep subsurface of the planet and even high temperature volcanic vents. Just as our understanding of microbial distribution has increased in recent years so has our appreciation of its importance. The goal of the EMI is to conduct innovative research examining the role of the microbial biome in regulating biological communities, geological processes, and environmental conditions. This applied and environmental research includes investigation of microbial communities in both pristine and highly altered ecosystems. It addresses issues of societal concern such as the dynamics of pathogenic bacteria in the environment, alterations in the functioning of ecosystems due to anthropogenic change, and the use of microbes for the elimination of waste or remediation of polluted ecosystems. In addition to studying the connection of microbial communities to today&rsquos regional and global environmental processes, Columbia&rsquos EMI aims to train young environmental scientists capable of addressing the environmental challenges of tomorrow.


Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

Keywords: horizontal gene transfer rhizobium-legume symbiosis.


Evolutionary History of Prokaryotes

Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

Microbial Mats

Microbial mats or large biofilms may represent the earliest forms of life on Earth there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes (Figure 2) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.

The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the Earth’s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely available energy source—sunlight—whereas others were still dependent on chemicals from hydrothermal vents for energy and food.

Figure 2. This (a) microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean in a region known as the “Pacific Ring of Fire.” The mat helps retain microbial nutrients. Chimneys such as the one indicated by the arrow allow gases to escape. (b) In this micrograph, bacteria are visualized using fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist credit b: modification of work by Ricardo Murga, Rodney Donlan, CDC scale-bar data from Matt Russell)

Stromatolites

Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat (Figure 3). Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.

Figure 3. (a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young credit b: P. Carrara, NPS)

The Ancient Atmosphere

Figure 4. This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are green, and as water flows down the gradient, the intensity of the color increases as cell density increases. The water is cooler at the edges of the stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-Mariño)

Evidence indicates that during the first two billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen—anaerobic organisms—were able to live. Autotrophic organisms that convert solar energy into chemical energy are called phototrophs, and they appeared within one billion years of the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria (Figure 4) began the oxygenation of the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O2-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O2 is converted into O3 (ozone) and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O2 concentrations allowed the evolution of other life forms.

Practice Questions

Microbial mats __________.

  1. are the earliest forms of life on Earth
  2. obtained their energy and food from hydrothermal vents
  3. are multi-layered sheet of prokaryotes including mostly bacteria but also archaea
  4. are all of the above

The first organisms that oxygenated the atmosphere were

  1. cyanobacteria
  2. phototrophic organisms
  3. anaerobic organisms
  4. all of the above

Diversity In Microbial Communities


Microbes constitute about a third of the Earth's biomass and exhibit remarkable genetic diversity. In a majority of environments, microbes live as interacting communities. Yet, we know almost nothing about how microbial worlds communicate, evolve, share resources, interact with other organisms in the rhizosphere and in aquatic environments, and ultimately shape the landscape of the Earth. Our recent research on speciation and evolution of thermophilic cyanobacteria that thrive in the microbial mats of hot springs in Yellowstone National Park has set the stage for a move into challenging new territory. We now have full genome sequences of two dominant cyanobacteria (Synechococcus sp.) and a green, non-sulfur photosynthetic bacterium Roseiflexus sp. Analyses of these genomes and metagenomes (i.e. genetic repertoire of the whole community) have given us a first glimpse into the complexity of microbial populations. We also pioneered methods to investigate the pattern of gene expression, protein abundances and activities in these microbes over the day-night cycle and discovered daily changes that describe the key features of the energetics of the mat community over the diel cycle. There appear to be a complex, integrated regulatory network (signaled by light, anoxia, or circadian rhythms) that occurs within these interactive communities. There also appears to be metabolite/energetic exchange among the organisms in the mat, which suggests that hypotheses generated using pure laboratory cultures would require careful in situ analyses in parallel. This is one of the emerging, challenging and exciting areas in environmental biology.
Our initial physiological findings, coupled with the genetic diversity of microbes, provide a unique and exciting opportunity to explore, in real time, how evolution and adaptation work in the microbial world at temperatures exceeding 50oC. I believe that cyanobacterial interactions in the environment provide an excellent paradigm for dissecting the survival, functional diversity and evolution of microbial communities in a variety of harsh environmental settings and how the diversification within the community reflects the integrated utilization of limiting resources. The biogeochemical and regulatory processes underlying these microbial communities can now be queried by a number of sophisticated tools.


Measures of Diversity in Microbial Communities: One of the surprises of our investigation of microbial communities was the discovery of unexpected diversity at every level, from gene variants to the level of whole genome architecture. These findings raise fundamental questions that we can begin to tackle:
(i) how and why is bacterial diversity maintained and how do populations evolve?
(ii) how can our study of model organisms, (that are essentially clonal) which is an accepted and powerful paradigm benefit from the idea that in the environment genomic complexity is the norm, rather than the exception?

We are approaching these questions with the following methodolgies:
Exploiting comparative genomics/metagenomics: Comparative genomics/ metagenomics is a very powerful tool and with the advent of high throughput/low cost sequencing it is possible to explore this at a level that was not feasible even a few years ago. Even with our limited analysis we have seen that genomic variability is extensive in the closely related cyanobacteria that we study. Taking this to the next logical step requires a deeper focus on specific questions. One such example which we are currently pursuing is the adaptation of cyanobacteria to high temperatures. In the microbial mats, there is a gradient of temperature (from

50C to 70C) that the cyanobacteria have adapted to in various as yet unknown ways. This natural temperature gradient and moderately simple assemblage of organisms provides an excellent setting for probing this question.

Ecophysiology of cyanobacteria: Beyond comparative genomics lies the question of how these differences in gene content impact the ecophysiology of cyanobacteria in the environment. For instance, we identified an entire nitrogenase (nif) gene cluster in these organisms suggesting that these unicellular cyanobacteria may be capable of nitrogen fixation. Nitrogen fixation reduces nitrogen gas to biomass, and is of paramount importance in biogeochemical cycling of nitrogen. To address this point, we analyzed nif transcript levels and nitrogenase activity of the Synechococcus ecotypes, over the diel cycle in the microbial mat of an alkaline hot spring in Yellowstone National Park. Nif transcripts rise in the evening, with a subsequent decline over the course of the night. In contrast, the level of the NifH polypeptide remained stable during the night, and only declined when the mat became oxic in the morning. Nitrogenase activity was low throughout the night however, it exhibited two peaks, a small one in the evening and a large one in the early morning, when light began to stimulate cyanobacterial photosynthetic activity, but oxygen consumption by respiration still exceeded the rate of oxygen evolution. Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. This study, among others, suggests that a multi-faceted approach to understand microbial communities can provide insights into the regulation of metabolism. Combining eco-physiology with experiments using clean Synechococcus isolates is also an approach we are actively developing. We have recently characterized a number of responses of these isolates to nutrient stress and to high light.

Exploring diversity at the single cell level: Extending from our results from the microbial mats it might not be too much of a stretch to say that bacterial populations in the environment are genetically varied and far from clonal. This raises the obvious question of how we can best assess this variability. A few years ago we initiated a collaboration with Dick Zare’s group in Chemistry to exploit the power of microfluidic cell chambers and single cell capture, followed by capillary electrophoresis to count single molecules (in this case the highly fluorescent phycobiliproteins in cyanobacteria). This led to interesting observations of variability in phycobiliprotein content in single cells and the conclusion that clonality is not necessarily the norm (put in another way, it says that averaging cellular output, although powerful, can conceal these single cell variations).

RESOURCES/TOOLS AVAILABLE:
1. Complete genome sequences of two dominant cyanobacteria (Synechococcus sp.) and an abundant green, non-sulfur photosynthetic bacterium (Roseiflexus sp.).
2. Metagenome dataset (i.e. genetic repertoire of the whole community) of microbial populations in the hotsprings.

220 Mb of paired Sanger reads
3. In-house tools developed for comparative genomic analyses
4. Methods to directly measure expression of specific genes in situ
5. Measurements of light and oxygen levels directly in the mats (using microsensor technology developed by Michael Kuhl and others).
6. Axenic (pure) isolates of Synechococcus sp. grown under defined laboratory conditions

RELEVANT PUBLICATIONS (PDF version available under Publications)


High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau

Meng Xu, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.

Junling Zhang, Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.

Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, Hainan, China

Soil Biology Group, Wageningen University, Wageningen, The Netherlands

Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China

Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China

Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China

Meng Xu, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.

Junling Zhang, Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.

Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China

Meng Xu, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.

Junling Zhang, Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.

Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, Hainan, China

Soil Biology Group, Wageningen University, Wageningen, The Netherlands

Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China

Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China

Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China

Meng Xu, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.

Junling Zhang, Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.

Abstract

Soil microbes are directly involved in soil organic carbon (SOC) decomposition, yet the importance of microbial biodiversity in regulating the temperature sensitivity of SOC decomposition remains elusive, particularly in alpine regions where climate change is predicted to strongly affect SOC dynamics and ecosystem stability. Here we collected topsoil and subsoil samples along an elevational gradient on the southeastern Tibetan Plateau to explore the temperature sensitivity (Q10) of SOC decomposition in relation to changes in microbial communities. Specifically, we tested whether the decomposition of SOC would be more sensitive to warming when microbial diversity is low. The estimated Q10 value ranged from 1.28 to 1.68, and 1.80 to 2.10 in the topsoil and subsoil, respectively. The highest Q10 value was observed at the lowest altitude of forests in the topsoil, and at the highest altitude of alpine meadow in the subsoil. Variations in Q10 were closely related to changes in microbial properties. In the topsoil the ratio of gram-positive to gram-negative bacteria (G+:G−) was the predominant factor associated with the altitudinal variations in Q10. In the subsoil, SOC decomposition showed more resilience to warming when the diversity of soil bacteria (both whole community and major groups) and fungi was higher. Our results partly support the positive biodiversity-ecosystem stability hypothesis. Structural equation modeling further indicates that variations in Q10 in the subsoil were directly related to changes in microbial diversity and community composition, which were affected by soil pH. Collectively our results provide compelling evidence that microbial biodiversity plays an important role in stabilizing SOC decomposition in the subsoil of alpine montane ecosystems. Conservation of belowground biodiversity is therefore of great importance in maintaining the stability of ecosystem processes under climate change in high-elevation regions of the Tibetan Plateau.