Prokaryotes are microscopic organisms that lack a nucleus and other organelles that are found in eukaryotes. There are two main types of prokaryotes – bacteria and archaea. Both bacteria and archaea are ubiquitous in nature and can be found in a wide variety of environments, including soil.
Quick Answers
Yes, prokaryotes are found in soil. In fact, soil is teeming with prokaryotes, including bacteria and archaea. Some key points about prokaryotes in soil:
- Soil is estimated to contain up to 10 billion microbial cells per gram, the majority of which are prokaryotes like bacteria and archaea.
- The most abundant phyla of bacteria found in soil include Proteobacteria, Acidobacteria, Actinobacteria, and Firmicutes.
- Common archaea found in soil belong to phyla such as Crenarchaeota and Euryarchaeota.
- Prokaryotes play vital roles in soil nutrient cycles, decomposition, nitrogen fixation, and pathogen suppression.
- The prokaryotic community composition in soil varies across different climates, plant communities, and soil types.
Abundance and Diversity of Prokaryotes in Soil
Soil is an immensely diverse microbial habitat, home to a wide variety of bacteria, archaea, and other microorganisms. In fact, soil contains some of the most diverse microbial communities on Earth.
In a single gram of soil, there are estimated to be anywhere between 10 million and 10 billion microbial cells. The majority of these microbes are prokaryotes, including members of both bacterial and archaeal domains.
Thousands of different species of prokaryotes may exist in the soil of a small region. The abundance and diversity of prokaryotes varies across different soil types and environments. Some key factors influencing prokaryotic communities in soil include:
- Climate and weather
- Soil pH
- Nutrient levels and organic matter content
- Oxygen availability
- Agricultural practices
- Presence of plants and plant communities
- Land use history
In general, neutral and alkaline soils support a greater abundance and diversity of bacteria compared to acidic soils. Anaerobic soil environments also favor archaea.
Most Abundant Bacterial Phyla in Soil
Thousands of different bacterial species may be found in soil samples. However, soil bacterial communities tend to be dominated by four major phyla:
- Proteobacteria: This hugely diverse phylum accounts for around 30-50% of all soil bacteria. Key groups include Alpha-, Beta-, Gamma-, and Deltaproteobacteria.
- Acidobacteria: Abundant in many soils, acidobacteria favor more acidic conditions. They may account for over 20% of soil bacteria.
- Actinobacteria: This phylum includes many important decomposers and are key in organic matter turnover. They thrive in soils with high organic content.
- Firmicutes: Gram-positive bacteria that includes endospore-forming genera Bacillus and Clostridium. They do well in alkaline and arid soils.
Other common soil bacterial phyla include Bacteroidetes, Planctomycetes, Chloroflexi, Verrucomicrobia, and Gemmatimonadetes.
Common Archaeal Phyla in Soil
Compared to bacteria, less is known about the archaeal inhabitants of soil. However, some of the main phyla found include:
- Crenarchaeota: Tend to thrive in acidic soils. Genera include Sulfolobus and Thermoproteus.
- Euryarchaeota: Found across many soil types. Include methanogenic and halophilic archaea.
- Thaumarchaeota: Ammonia-oxidizing archaea, important in nitrogen cycling.
- Korarchaeota: Likely play a role in nitrification and carbon cycling.
Advances in DNA sequencing continue to uncover the diversity of archaea present in soils around the world.
Roles and Functions of Soil Prokaryotes
Prokaryotes drive many essential ecosystem services and geochemical processes in the soil environment. Here are some of their key roles:
Organic Matter Decomposition
Prokaryotes mineralize and decompose organic matter in soil, making nutrients available for plant uptake. Bacteria secrete enzymes that break down complex polymers such as cellulose, chitin, and lignin. Acidobacteria, Actinobacteria, and Proteobacteria are especially important.
Nutrient Transformations
Prokaryotes drive major biogeochemical cycling in soil, including nitrogen, carbon, phosphorus, and sulfur transformations. Examples include:
- Nitrogen fixation: Conversion of N2 gas to ammonia by diazotrophs.
- Nitrification: Oxidation of ammonia to nitrites/nitrates by nitrifying bacteria and archaea.
- Denitrification: Respiratory reduction of nitrate to N2 gas.
- Phosphorus solubilization: Making insoluble phosphorus available to plants.
Suppression of Pathogens
Many soil prokaryotes produce antibiotics and compete with pathogens, preventing disease. Examples include Pseudomonas, Streptomyces, Bacillus species.
Soil Structure Formation
Prokaryotic secretions help bind soil particles into aggregates and improve soil structure. Exopolysaccharides produced by cyanobacteria help stabilize soil.
Other Roles
Soil prokaryotes also:
- Improve soil health and fertility.
- Allow plant growth by fixing nitrogen.
- Protect plants by preventing root diseases.
- Aid in bioremediation and detoxification.
- Sequester carbon through biomass.
Factors Influencing Soil Prokaryotes
Many biotic and abiotic factors shape the prokaryotic communities present in soil. These include:
Soil pH
Soil pH strongly influences microbial composition, with acidic soils favoring acidobacteria and alkaline soils favoring Actinobacteria.
Climate and Temperature
Climate affects moisture, salinity, and other conditions for soil microbes. Higher temperatures speed up microbial growth and activity.
Nutrient Availability
Nutrient levels shape prokaryotic metabolism, growth, and activity. Availability of carbon, nitrogen, and minerals all play a role.
Soil Porosity and Structure
Well-aggregated, porous soils allow air and water flow needed for aerobic prokaryotes. Dense or compacted soils limit microbial life.
Agricultural Practices
Tilling, fertilizer use, planting crops in rotations, and pesticides alter microbial communities. Sustainable practices enrich native prokaryotes.
Plant Communities
Plants shape the rhizosphere environment. Prokaryotes interact closely with plant roots through the release of exudates.
Moisture Content
Moisture levels impact microbial activity. Floods and droughts disturb prokaryotic communities through osmotic stress.
Studying Prokaryotes in Soil
Traditionally, soil prokaryotes were studied by culturing techniques. However, over 99% of soil microbes cannot be cultured. Newer methods include:
- DNA sequencing: Sequencing marker genes like 16S rRNA identifies microbial taxa present.
- Metagenomics: Sequencing total DNA reveals functional potential of the microbiome.
- Microscopy: Scanning electron microscopy reveals microbial shapes and associations.
- Lipid analysis: Measures signature lipids in cell membranes to identify taxa.
- Culturing: Growing prokaryotes in lab to study physiology and metabolites.
These techniques continue to uncover the immense diversity of prokaryotes in soils around the world.
Examples of Important Soil Prokaryotes
Here are some examples of key prokaryotic groups in soil and their roles:
| Group | Example Genera | Significance |
|---|---|---|
| Rhizobia | Rhizobium, Bradyrhizobium | Nitrogen fixation in root nodules of legumes |
| Nitrifying bacteria | Nitrosomonas, Nitrobacter | Oxidize ammonia and nitrites in nitrogen cycle |
| Denitrifiers | Pseudomonas, Bacillus | Anaerobic respiration converting nitrates to N2 gas |
| Mycorrhizal fungi | Glomus, Laccaria, Tricholoma | Symbiotic associations with plant roots |
| Cellulose decomposers | Cellulomonas, Cytophaga | Secrete cellulases to decompose plant matter |
| Actinobacteria | Streptomyces, Micromonospora | Antibiotic production and organic matter decomposition |
| Cyanobacteria | Anabaena, Nostoc | Nitrogen fixation, soil aggregation |
This table highlights just a few groups of the myriad prokaryotes that populate soils and enable ecosystem functioning.
Distribution of Soil Prokaryotes
Prokaryotes live not only on soil particle surfaces, but also colonize tiny micro- and nanopores within soil aggregates. This allows them access to water films and organic matter.
Larger bacterial species tend to colonize the surfaces of larger soil particles like sand. Smaller bacteria populate the micro- and nanopores between smaller silt and clay particles.
Prokaryotes clustered near plant roots in the rhizosphere benefit from the nutrients in root exudates. Fungal hyphae also serve as highways allowing prokaryotic dispersal through soil.
Vertical Distribution
In terms of depth, prokaryotes tend to be most abundant near the soil surface where fresh organic matter and oxygen are more available. Numbers generally decrease deeper down the soil profile, but prokaryotes can be found many meters down.
Hotspots
Prokaryotes concentrate in certain soil hotspots that provide preferable microconditions. Hotspots include:
- Plant roots and the rhizosphere
- The drilosphere around earthworm burrows
- Decomposing organic matter like litter or manure
- Soil aggregates and pores
These hotspots support orders of magnitude higher prokaryotes than the surrounding soil matrix.
Impacts of Agriculture on Soil Prokaryotes
Modern agricultural practices can dramatically alter the prokaryotic communities in soil. Some impacts include:
- Tillage: Physical disturbance and increased aeration from plowing.
- Fertilizers: Shift microbial populations and provides extra nutrients.
- Pesticides: Toxic effects on beneficial prokaryotes.
- Monocrops: Reduces plant diversity and root exudates.
- Grazing: Removal of vegetation and compaction from livestock.
Sustainable practices like cover crops, rotational grazing, and no-till farming can help support healthy, diverse soil prokaryotes.
Prokaryotes in Extreme Soil Environments
Prokaryotes thrive even in harsh, extreme soil environments across the world:
Hot & Arid Desert Soils
Desert crusts host Proteobacteria, Cyanobacteria, and Actinobacteria adapted to heat, UV radiation, and desiccation.
Wetland Soils
Anaerobic bacteria and methanogenic archaea generate methane in waterlogged wetland soils.
Permafrost Soils
Cold-adapted Actinobacteria, Proteobacteria, and Bacteroidetes survive frozen conditions for millennia in permafrost.
Acidic Forest Soils
Acidobacteria and Alpha-Proteobacteria tolerate acidic, low-nutrient soils like boreal forest podzols.
Saline Soils
Halophilic archaea and salt-tolerant bacteria inhabit hypersaline soils.
These examples highlight the impressive adaptability of prokaryotes to grow across a vast range of soil environments.
Conclusion
In conclusion, prokaryotes including bacteria and archaea are ubiquitous members of soil microbial communities across virtually all terrestrial ecosystems on Earth. The great abundance, diversity, and versatility of soil prokaryotes drive crucial biogeochemical cycles and allow plant productivity. Although there is still much to learn, current molecular tools continue to reveal the hidden diversity of these essential microorganisms beneath our feet.
