BY : K. Sai Manogna (MSIWM014)


For microorganisms, soils are widespread and essential ecosystems that play crucial roles in providing plants with nutrients. If you dig a hole in the earth, you will find that the ground has a structure with various levels of evidence. These include the top organic horizon (O horizon), which includes freshly fallen litter on top by partially decomposed organic matter lower down, followed by horizon A, which comprises a range of minerals. The horizon B where humus, clays, and other materials transported live, and finally, the weathered parent material horizon C. With thin soils overlying calcareous regions of the world, such as the Yucatan, and dense soils occurring in some of the rich farmlands, such as those found in the Midwestern United States, the depth of these layers can differ drastically. Areas where heavy rainfall occurs, have nutrient-poor soils, such as the tropics, and over time the rains leach nutrients from the soils. The degree to which nutrients and microorganisms can travel can influence the permeability of the soil. Light does not penetrate beneath the first centimetre or two, eliminating phototrophy as a means of energy acquisition. The rhizosphere, the region around plant roots, is a habitat where abundant microbial populations occur.

Microbial Food Webs:

One of the greatest treasures of novel species is antibiotics and insights into how populations are organized in soil ecosystems on earth. On average, there are 109 bacterial cells in one gram of soil representing up to 5000 [or even 10,000] bacterial species by some estimates. The nature of soil food web and its inhabitants are more complicated than you might think. Plants play a significant role in physically structuring the under-ground ecosystem through their roots and the impact of their aboveground canopy, depending on the aridity of the aboveground environment. The larger organisms in the soil, such as earthworms, mites, springtails, nematodes, protists, and other invertebrates, were the subject of much of the soil biota research. These species help ‘engineer’ the soil conditions through their absorption and excretion of soil sections. On the scale of the microenvironment, bacteria and fungi even serve as engineers.

Soil microbial abundance varies with the microenvironment’s physical and chemical characteristics, including the content of moisture, organic matter abundance, and the size of soil aggregates. Although seasonal changes contribute to the dynamics of microbial soil populations, discussions of soil microorganisms typically refer to the topsoil sampled during the growing season. The most abundant microorganisms in the soil follow this sequence, as determined by plate count methods:

Algae < Fungi < Actinomycetes = Anaerobic bacteria < Aerobic bacteria

Microorganisms are most common on the surface and decrease as the depth increases in colony-forming units. In the variety of physiological forms of bacteria in various soil environments, soil types, including different organic content and related microbial processes, are seen. There is a substantial genetic diversity of bacteria in soil, and many of the physiological classes still have to be cultivated in the laboratory. Thus, molecular techniques produce more knowledge than conventional plating exercises for the study of the soil culture.

Soils comprise almost all the main microbial groups: bacteria, viruses, fungi, and archaea. Progress has been made in delineating which groups are most prevalent using culture-independent approaches in soil societies. Thirty-two different libraries of sequences from different soils were studied. Their results are impressive: 32 different phyla were present in the tests, but nine phyla were dominant: Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, Gemmatimonadetes, and Firmicutes. Proteobacteria account for the highest percentage of soils (39 percent on average). The majority of the sequences were new, and the results of this study vary significantly from the cultivation studies found in previous decades.

Symbiotic nitrogen fixers and mycorrhizae, which provide 5-20 percent of grassland and savannah nitrogen and 80 percent of nitrogen in temperate and boreal forests, are two main classes of bacteria in soil have been extensively studied. Nitrogen and phosphorus derived from symbiotic microorganisms are dependent on at least 20,000 plant species. Plants require nitrogen, and they are unable to fix atmospheric nitrogen in a beneficial form without their symbiotic partners. Examples of essential nitrogen-fixing bacteria are Frankia, an actinomycete that is important in forest growth, and Rhizobium, a key player in the health of crop legumes. These trees may grow in more marginal areas where nitrogen is restricted by interactions between plants, such as the alder tree (Alnus) and Frankia. More than 25 different genera of trees and shrubs have been recorded for cultivation in association with Frankia. Chemoheterotrophs, free-living in the soil or associated with a broad range of legumes, including alfalfa, clover, lupines, and soybeans, are rhizobia, including Azorhizobium, Bradyrhizobium, and Rhizobium. In order to infect them, plants release chemical compounds to attract soil rhizobia. On root hairs, most of the nodules form, but some form on stems. Nodules can use 7-12 percent of the plant’s photosynthetic production when active, but the expense is well worth the return in the form of fixed nitrogen available to the plant.

Despite the progress in understanding soil food webs, our understanding of soil food webs’ mechanisms is hindered by significant challenges. Different feeding classes are generally aggregated because, in their feeding patterns, most soil species are very “flexible,” muddling the distinctions between trophic stages. Relatively unknown are the diets of tiny species. New molecular techniques such as fluorescent in situ hybridization are exciting instruments that can help to expose the dynamic relationships in the soil population of who eats whom. Another instrument that is used to expose feeding relationships and energy sources is stable-isotope analysis.


BY: K. Sai Manogna (MSIWM014)

For a human being who is 890,000 times larger than an E.coli cell, it is difficult to think of microbial environments on the order of micrometres to thousands of meters. Conditions like oxygen or pH will drastically change over this time. It creates microenterprises, and ecosystems are therefore more patchy than stable. Different abiotic factors influence and help establish these microenvironments in microbial communities in these habitats. Any disruption can lead over time to changes in microbial populations in habitats.

Table: Effects of abiotic factors:

Abiotic factorsRange of States
O2 LevelAnoxic-microoxic-oxic
Moisture levelArid-moist-wet
Light levelAphotic-low level-bright-UV

The Niche:

The ‘niche’ turning to the general ecological literature shows that there is what is known as the ‘fundamental niche,’ which reflects all environmental factors. In the ecosystems, the environment affects a species’ ability to survive and reproduce in the environment. The ‘realized niche’ is also the proper niche when biotic interactions (i.e., competition) restrict a species’ growth and reproduction. The definition of niche has been extended to microscopic organisms, enabling bacteria and archaea to exploit new niches not available to parentage by acquiring new genes through horizontal transmission. This niche definition for bacteria and archaea focuses more on the organism’s acquisition of new functional ability by transmitting horizontal genes, which implies a more complex character for niche boundaries. The survival and best reproduction niche of Ferroplasma are characterized by acidic, stable, rich in iron and heavy metals, and moderate temperatures. These conditions distinguish Ferroplasma’s niche space. Species also may change their climate so that other species have a more or less habitable environment.

Aquatic Habitats:

The oceans and flowing water bodies, for example, rivers and streams, range in aquatic ecosystems. Water, more than 97% found in the world’s oceans, covers nearly 71 percent of the earth’s surface. In streams, rivers, and lakes, less than 1 percent of water is contained. Water is continuously renewed through the hydrological cycle in all those various marine ecosystems. The scale of aquatic environments and their diversity suggests the significance for microorganisms of aquatic habitats. Key microbial players in aquatic environments include primary production phototrophs and the heterotrophs involved in carbon cycling in aquatic habitats.

In these marine settings, the environmental and physicochemical conditions vary greatly. Water movement is one of the apparent factors; streams and rivers will flow quickly, with lakes moving less. Winds produce surface water movement in the seas, create ocean waves, and create upwelling areas. These winds transfer nutrients, organisms, oxygen, and heat worldwide, in addition to deep-water currents. As in the seas, water circulation in all marine environments determines different properties of water. Physicochemical factors, such as the pH, the abundance and availability of macro-and micronutrients, salinity, phosphorus, nitrogen, sulphur, and carbon, can vary significantly within the various ecosystems.

Table: Characteristics of different aquatic habitats:

Aquatic habitatTemperature rangeSalinity (%)
Oceans-1.5 to 27oC at surface3.5
a. freshwater
b. great salt lake


avg. 12%

Storms are very fluid, have significant variations in physical and chemical environments, are greatly affected by their drainage range, and have a single water flow. In contrast, the lakes, particularly the stream’s headwaters, have more stable conditions and primary productivity. Lakes can be acidic or alkaline (e.g., Mono Lake, California), but often they can be saltier than freshwater, like the Great Salt Lake, Utah.

Aquatic microbial ecology has been advanced from descriptive research on who’s home” to hypothesis-driven studies of interactions and environmental and biological controls on the diversity and population distributions. A broad range of anti-predating mechanisms, including the secretion of exopolymer substances and capsules made up of polysaccharides and morphologic adaptations, are two of the exciting features and the subject of several studies. They are gram-positive. Studies have focused on how predators evade microbial communities, like predation, particularly by protists, and virus lysis is a significant mortality factor. Viruses in various aquatic environments are standard, with a difference of between one or two orders in size in these different habitats, while in freshwater, the abundance of the virus is more seasonal. In aquatic settings, what governs viral abundance is still under review.  In aquatic environments, viruses have a vital role in recovering organic matter dissolved by lysing their presence into their bodies, converting the carbon and other nutrients.

a. Fresh Water

The word wetlands for freshwater generally applies to rivers, streams, reservoirs, lakes, and groundwater. Freshwater that contains less than 1.000 mg/ l dissolved solids is classified under the United States Geological Survey (USGS). As noted above, freshwater microorganisms vary greatly from marine environments in their phylogenetic diversity. Typical freshwater bacterial classes include beta-proteobacteria (e.g., the relative of Rhodoferax and Polynucleobacter necessarius), Actinobacteria, Cytophaga/Flexibacter/Flavobacterium hydrolysis relatives.

b. Lakes:

Lakes are aquatic lakes, initially formed by glaciation, volcanism, or tectonics. The Great Lakes in North America, and Lake Baikal, Siberia, comprise approximately 40% of the world’s freshwater at a few vast lakes.

There are many gradients within water bodies that affect microbial distribution populations. The oxygen gradient is one of the most critical. In lakes where upper waters can be oxic and warmer, the lower gradient is colder and often anoxic. The thermocline is separated by these two layers, which is a transition region between the two layers. Seasonal changes in atmospheric temperature and water temperature can result in changes in density that turn the water over and allow oxygenated water to enter the lake’s lower reaches. It influences the microbial communities of the lake.

The vegetation around lakes supplies some nutrients that have been found in lakes. Low nutrient quantity lakes are oligotrophic, while high nutrient quantities, productivity, and oxygen depletion can affect species that can survive under such conditions. Lakes are eutrophic. The transformation of contaminants such as sulphur dioxide and nitrous oxide (NO3) into acid rain causes some lakes to be naturally acidic while other acidic. Lakes in North-East America recover from acid rain impacts. The pH of the water in lake also influences the population of microbes.

c. Rivers and Streams:

During and after a rainstorm, the water will change and get a water movement force in rivières. Water is moving in streams and rivers through vast material, soil, trees, rocks, and other substances. It ensures a steady supply of nutrients to biotic communities and a great deal of trouble during floods. Many rivers cross cities and thus are exposed to human wastewater and other contaminants that can directly affect the river’s population. As the metabolic diversity of microorganisms is such that specific contaminants are potential energy sources in microorganisms. Since high organic loading can result in high productivity that diminishes oxygen levels, areas of urban rivers can be anoxic, limiting microorganisms in such regions.

The ecosystem of the river consists of many components like horizontal

(1) the active channel that can go dry part of the year in some rivers and streams and

(2) the transitional zone between the marine and the terrestrial habitats, in the riparian zone.

Vertically, streams and rivers are marked by

(1) Waters of the surface;

(2) the sub-surface water region of the hyporheic zone;

(3) the phreatic groundwater field.

The physicochemical properties of these ecosystems differ. Rivers and streams have many suspended organic and inorganic particles, restricting how much light penetrates the water column. At least partly shaded by trees that hang over the streams, the parts of the reaches have extensive vegetation. The extent of photosynthesis in the streams is restricted by both turbidity and shading. Desert streams are much higher than in tropical and temperate regions and have no shading of microbial photosynthesis. Rivers and rivers differ in their salinity by order of magnitude; desert rivers have the highest amounts.

d. Hot Springs:

Springs are springs of geothermal water, groundwater which comes into contact with hot rocks or magma from the world’s earth’s crust in volcanically active regions. Some impressive examples are found in Yellowstone’s national park in Wyoming, Iceland, Japan, and New Zealand.  Hot springs reflect extreme temperature conditions and, in some cases, pH. There is a high concentration of anaerobic or microaerophilic hot spring that suggests low oxygen concentrations. In hot springs where temperature limits are photosynthesis, they were suggested to be primordial producers. Hyperthermophiles, who use carbon dioxide as their carbon source, are also chemoautotrophs and serve as primary producers within hot spring ecosystems. Hot springs contain various gases, including molecular hydrogen and a reduced number of iron and sulphur compounds, dissolved and provide electron donors. It implies that Yellowstone’s primary productivity results from molecular hydrogen oxidation, which can happen to levels above 300 nM. in hot springs. Hot springs are the prime habitat for archaeological animals.

Marine habitats:

a. Oceans: 

In addition to the fact that it is a saline ocean rather than a terrestrial habitat. It is one of several environmental parameters that influence the existence of marine habitat microorganisms. Furthermore, temperature, light, food supply, and pressure vary from the surface to the ocean’s depths. The ecosystems of the ocean shift from shore to vertical depth. Traveling further into the water, from the surface or epipelagic region to the mesopelagic zone (200–1000m), you move into the bathypelagic zone (1000–4000m), the abyss area (4000–6000m), and eventually the Hadean area (<6000m).

b. Food and Microbial Aquatic Habitats:

The marine food web is typically characterized by the low nutrient abundance and patchy nature of the gradients, as mentioned above, and high salinity.

Although the food web has been studied on the ocean for more than a hundred years, several recent findings have led us to believe that the classical description of a chain from diatoms through copepods and to fish and whales can only be a small part of the energy flow. Recent studies of microorganisms, organic dissolved matter, and organic particles in the sea have shown other mechanisms by which a significant share of the energy available will flow. For decades, marine scientists have been cautiously approaching this food web view, and care should be taken when a paradigm is challenged.