Biodiversity
Microbial Biodiversity
Biodiversity is critical to the health and sustainability of our planet’s ecosystems, including agricultural systems. Monitoring and measuring biodiversity in agriculture can help us understand the status and trends of the diversity of living organisms within a given ecosystem, and how that diversity is affected by agricultural practices.
Sequencing technologies can be applied to identify the microbes in a sample and calculate the diversity of its microbiome community. When we do so, we talk about “alpha diversity”. See more below on how we calculate alpha diversity as a measure of biodiversity or biotic diversity.
Why monitor or measure biodiversity in agriculture?
Here are some key reasons why monitoring or measuring biodiversity in agriculture is important:
1. Ecosystem health: Biodiversity is critical to the health and resilience of agricultural ecosystems. A diverse range of organisms, from microbes and insects to birds and mammals, play important roles in regulating soil fertility, pollination, pest control, and nutrient cycling. When biodiversity is compromised, these vital ecosystem services may be disrupted, leading to decreased crop yields, degraded soil quality, and increased reliance on synthetic inputs.
2. Sustainability: Maintaining biodiversity is essential to the long-term sustainability of agricultural systems. A lack of biodiversity can lead to decreased productivity, increased vulnerability to pests and diseases, and soil degradation. By monitoring and measuring biodiversity, we can better understand how agricultural practices are impacting biodiversity and make informed decisions about management strategies that can promote long-term sustainability.
3. Food security: Agricultural biodiversity is also critical to global food security. Genetic diversity in crops can help to ensure that they are able to adapt to changing environmental conditions, such as climate change or disease outbreaks. Additionally, maintaining diverse agroecosystems can help to ensure that a range of crops and agricultural products are available to meet the nutritional needs of people around the world.
4. Climate change: Biodiversity can also play a critical role in mitigating the impacts of climate change. For example, diverse plant communities can sequester more carbon from the atmosphere, which can help to reduce greenhouse gas emissions. By monitoring and measuring biodiversity, we can better understand how agricultural practices can contribute to climate change mitigation efforts.
5. Policy and decision-making: Monitoring and measuring biodiversity in agriculture can also help inform policy and decision-making. By understanding the status and trends of biodiversity, policymakers can make informed decisions about land use, conservation, and management practices that can promote biodiversity conservation and sustainable agriculture.
In conclusion, monitoring and measuring biodiversity in agriculture is critical for maintaining healthy and sustainable agricultural ecosystems, promoting food security, mitigating climate change, and informing policy and decision-making. By paying close attention to biodiversity in agriculture, we can ensure that our agricultural systems are able to provide for our nutritional needs while preserving the health of our planet’s ecosystems.
We used BiomCare to analyse faecal samples collected in a project assessing the role of diet in the development of the infant gut microbiota in Peru.
We felt supported throughout the project by BiomCare, with Louise and the team going above and beyond to assist with any queries. We were provided with regular updates on the status of our analysis and all communications were clear and timely.
The data was presented within accessible reports, making the results easy to interpret. We would strongly recommend BiomCare for any microbiome analysis.
Megan Stanley
PhD students, Loughborough University, UK
Sequencing methods to measure biodiversity
In its simplest form, biodiversity describes the number of different living organisms in a system. But this is only one of a range of measures for biodiversity that can be calculated from sequencing data.
At Biomcare, we use sequencing to study diversity, and based on the sequencing data calculate different biodiversity measures to evaluate the diversity from different perspectives. However, they all fall within one of the following groups:
- Richness – the number of different species in a given sample
- Inferred richness – the number of different species in a given sample, when considering the organisms that we did not detect due to technical limitations.
- Evenness – the degree to which the relative abundances of the different species in the sample are similar
- Or a combination of richness and evenness – that is measures that consider both richness and evenness
At Biomcare we calculate several different measures to cover the different interpretations and make sure we fully elucidate the properties of the biodiversity in a given sample. When we have calculated alpha diversity, we apply statistics to understand if the diversity is significantly different between conditions or associated with an external factor of interest.
The sequencing methods used dictate what part of the community is studied:
- Amplicon methods (aka. Metabarcoding) capture a subset of the microbiome depending on the genetic region that is sequenced e.g. bacteria with 16S and fungi with ITS. Amplicon sequencing allow us to consider all detected microbial entities based on the code of the genetic region and therefore allow us to include microbes that are unknown or are not found in reference databases. Therefore, the diversity measure obtained using amplicon is often higher than the measure obtained with shotgun metagenomic data where the diversity measures represent the diversity of known organisms.
- Shotgun metagenomic capture all living organisms only limited by their abundance (the more data we generate for a sample the lower abundant organisms will be captured). We can therefore get a picture of the diversity that include cross-kingdom taxa such as both bacteria and fungi, however for diverse communities a deep sequencing is needed to capture the full diversity. To identify microbial entities with this data we rely on reference databases, and consequently the diversity measure only represents the diversity of known microbes. Note there are exceptions to this rule, where for low complexity samples we can use reference-free processing and capture unknown organisms.
To complicate things, biodiversity can be analyzed using several other techniques. Each technique capture an aspect of diversity and they are often not directly compatible. It is therefore important to consider which methods is used and what information or aspect of biodiversity it provides.
The concept of biodiversity
Biodiversity can describe the diversity of living organisms in a larger environment like the ocean, in a more specific location like a lake, field, or forest, but also the diversity of a type of organisms like plants, fishes, or microorganisms. Biodiversity can also broadly describe the general variety of life on earth through different ecosystems on the planet, such as deserts, rainforests, and coral reefs. Furthermore, biodiversity considers the diversity within a species, such as its genetic diversity and many dimensions must thus be considered when fully assessing biodiversity.
Therefore, what is exactly meant by biodiversity depends on the connection in which the term is used.
People concerned with the quality of freshwater lakes will discuss the diversity as the number of different fish in the water and perhaps include information on the total number of fish. Or they will discuss the number of different microorganisms in the water well knowing these tiny living organisms are important indicators for the quality of the water.
Biodiversity and sustainability
The term biodiversity will often be heard in connection to discussions of sustainable farming, pollution, and climate changes. This is because pollution and climate change are known to reduce the diversity of living organisms on the planet, and in environments like the soil and water. Biodiversity enhances the productivity of an ecosystem – because each species, no matter how small, has an important role to play.
In ecology, involving the interaction between living organisms, concepts such as cooperation and competition are important and we recognize how “survival of the fittest” is important to keep a balanced ecosystem. Despite the competition between species, each species depend on the services provided by others to survive. Appropriate conservation and sustainable development strategies, therefore, recognize the need to preserve and increase biodiversity.
Declining biodiversity is a concern for many reasons. In recent years the reduction in the diversity of insects has been a highly discussed topic, especially with a focus on the reduction in the number of bees due to high usage of pesticides.
News channels around the world have not dedicated their time to discussing the reduction in the numbers and diversity of bees solely due to our liking for honey. A statement from the German bee expert Professor Joergen Tautz from Wurzburg University made the importance of bees to our ecosystem very clear when he in an interview stated:
“Bees are vital to biodiversity. There are 130,000 plants for example for which bees are essential to pollination, from melons to pumpkins, raspberries, and all kinds of fruit trees — as well as animal fodder — like clover. Bees are more important than poultry in terms of human nutrition.”
The Telegraph, March 14, 2007
Humans are using an increasing fraction of the earth’s surface for farming. While this is necessary to feed the growing population, it is also causing serious risks to our ecosystems and the biodiversity of the nature around us. When a single crop is grown on a field, the diversity of the field is drastically reduced. As a consequence, many plants that are not used for human or animal food, but which are important for our ecosystem, are having a hard time finding a place to grow.
This reduces both the diversity of plants and insects, as well as bigger animals living wild in nature, as their natural habitats are reduced. But also, the diversity of the smaller organisms, the microorganisms in the soil, is suffering. The fertilization, use of pesticides, and intense usage of the soil cause the diversity of microorganisms to decline. This has the critical consequence of reducing the health of the soil and its ability to support the production of plants for food for the world’s larger living beings.
“Bees are vital to biodiversity. There are 130,000 plants for example for which bees are essential to pollination, from melons to pumpkins, raspberries, and all kinds of fruit trees — as well as animal fodder — like clover. Bees are more important than poultry in terms of human nutrition.”
The Telegraph, March 14, 2007
Biodiversity is key for agriculture
The interaction between soil, plants, and microorganisms, including bacteria and fungi, is fundamental for the plant’s ability to take up nutrients from the soil. In turn, the diversity of microorganisms in the soil is key to effective agriculture. Soil degradation by pollution, depletion, contamination, salinization, etc., destroys the habitat of soil organisms and causes soil biodiversity to decrease. Key factors of management practices that reduce soil diversity include reduced deposition of organic matter and the sidestep of naturally occurring nutrient cycling by microorganisms.
One key example of the importance of soil biodiversity is the role of microorganisms in the nitrogen cycle. Nitrogen is found in the environment in several different chemical forms such as organic nitrogen, ammonium, nitrite, nitrate, or inorganic nitrogen gas. Organic nitrogen is found in living organisms such as plants and animals, in humus, or intermediate products. In the nitrogen cycle, nitrogen is transformed from one form to another, and many of those transformations are carried out by microbes. Microorganisms carry out the processes of transforming nitrogen for their benefit, but the processes are essential for the cycling of the important building block. Of key importance to farming is the breakdown of the nitrogenous components in animal urine by nitrifying bacteria in the soil so that the nitrogen can be used by plants.
It is important to understand the factors that affect soil diversity, the roles of the many diverse organisms, and to learn how we can support the soil’s natural diversity so that the naturally occurring soil processes can support sustainable agriculture.
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We used Biomcare to analyse the occurrence and composition of bacteria and fungi in soil samples, in a project evaluating soil fertility and the effect of tilling.
BIOMCARE was involved from study design, over shipment, sequencing, data analysis and interpretation.
The results were presented in easily understandable and illustrative reports, and by personal communication, and all communication went swiftly.
I can highly recommend BIOMCARE for their expertise.
Annette Vibeke Vestergaard
Senior specialist - soil and soil management. Crop Innovation and Environment, SEGES