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Sphingomonadaceae are a gram-negative bacterial family of the Alphaproteobacteria. An important feature is the presence of sphingolipids in the outer membrane of the cell wall. The cells are ovoid or rod-shaped. Others are also pleomorphic, i.e. the cells change the shape over time. Some species from Sphingomonadaceae family are dominant components of biofilms.
An arbuscular mycorrhiza (AM) is a type of mycorrhiza in which the symbiont fungus penetrates the cortical cells of the roots of a vascular plant forming arbuscules.
Paenibacillus is a genus of facultative anaerobic, endospore-forming bacteria, originally included within the genus Bacillus and then reclassified as a separate genus in 1993. Bacteria belonging to this genus have been detected in a variety of environments, such as: soil, water, rhizosphere, vegetable matter, forage and insect larvae, as well as clinical samples. The name reflects: Latin paene means almost, so the paenibacilli are literally "almost bacilli". The genus includes P. larvae, which causes American foulbrood in honeybees, P. polymyxa, which is capable of fixing nitrogen, so is used in agriculture and horticulture, the Paenibacillus sp. JDR-2 which is a rich source of chemical agents for biotechnology applications, and pattern-forming strains such as P. vortex and P. dendritiformis discovered in the early 90s, which develop complex colonies with intricate architectures as shown in the pictures:
The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. The rhizosphere involving the soil pores contains many bacteria and other microorganisms that feed on sloughed-off plant cells, termed rhizodeposition, and the proteins and sugars released by roots, termed root exudates. This symbiosis leads to more complex interactions, influencing plant growth and competition for resources. Much of the nutrient cycling and disease suppression by antibiotics required by plants, occurs immediately adjacent to roots due to root exudates and metabolic products of symbiotic and pathogenic communities of microorganisms. The rhizosphere also provides space to produce allelochemicals to control neighbours and relatives.
Soil solarization is a non-chemical environmentally friendly method for controlling pests using solar power to increase the soil temperature to levels at which many soil-borne plant pathogens will be killed or greatly weakened. Soil solarization is used in warm climates on a relatively small scale in gardens and organic farms. Soil solarization weakens and kills fungi, bacteria, nematodes, and insect and mite pests along with weeds in the soil by mulching the soil and covering it with a tarp, usually with a transparent polyethylene cover to trap solar energy. This energy causes physical, chemical, and biological changes in the soil community. Soil solarization is dependent upon time, temperature, and soil moisture. It may also be described as methods of decontaminating soil or creating suppressive soils by the use of sunlight.
The laimosphere is the microbiologically enriched zone of soil that surrounds below-ground portions of plant stems; the laimosphere is analogous to the rhizosphere and spermosphere. The combining form laim- from laimos denotes a connecting organ (neck) while -sphere indicates a zone of influence. Topographically, the laimosphere includes the soil around any portion of subterranean plant organs other than roots where exuded nutrients stimulate microbial activities. Subterranean plant organs with a laimosphere include hypocotyls, epicotyls, stems, stolons, corms, bulbs, and leaves. Propagules of soil-borne plant pathogens, whose germination is stimulated by a plant exudates in the laimosphere, can initiate hypocotyl and stem rots leading to "damping-off". Pathogens commonly found to cause such diseases are species of Fusarium, Phoma, Phytophthora, Pythium, Rhizoctonia and Sclerotinia.
Rhizobacteria are root-associated bacteria that can have a detrimental, neutral or beneficial effect on plant growth. The name comes from the Greek rhiza, meaning root. The term usually refers to bacteria that form symbiotic relationships with many plants (mutualism). Rhizobacteria are often referred to as plant growth-promoting rhizobacteria, or PGPRs. The term PGPRs was first used by Joseph W. Kloepper in the late 1970s and has become commonly used in scientific literature.
Microbial inoculants also known as soil inoculants or bioinoculants are agricultural amendments that use beneficial rhizosphericic or endophytic microbes to promote plant health. Many of the microbes involved form symbiotic relationships with the target crops where both parties benefit (mutualism). While microbial inoculants are applied to improve plant nutrition, they can also be used to promote plant growth by stimulating plant hormone production.
A biofertilizer is a substance which contains living micro-organisms which, when applied to seeds, plant surfaces, or soil, colonize the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant. Biofertilizers add nutrients through the natural processes of nitrogen fixation, solubilizing phosphorus, and stimulating plant growth through the synthesis of growth-promoting substances. The micro-organisms in biofertilizers restore the soil's natural nutrient cycle and build soil organic matter. Through the use of biofertilizers, healthy plants can be grown, while enhancing the sustainability and the health of the soil. Biofertilizers can be expected to reduce the use of synthetic fertilizers and pesticides, but they are not yet able to replace their use. Since they play several roles, a preferred scientific term for such beneficial bacteria is "plant-growth promoting rhizobacteria" (PGPR).
Agricultural microbiology is a branch of microbiology dealing with plant-associated microbes and plant and animal diseases. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations.
A microbial consortium or microbial community, is two or more bacterial or microbial groups living symbiotically. Consortiums can be endosymbiotic or ectosymbiotic, or occasionally may be both. The protist Mixotricha paradoxa, itself an endosymbiont of the Mastotermes darwiniensis termite, is always found as a consortium of at least one endosymbiotic coccus, multiple ectosymbiotic species of flagellate or ciliate bacteria, and at least one species of helical Treponema bacteria that forms the basis of Mixotricha protists' locomotion.
Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.
The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.
The phycosphere is a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell. This area is high in nutrients due to extracellular waste from the phytoplankton cell and it has been suggested that bacteria inhabit this area to feed on these nutrients. This high nutrient environment creates a microbiome and a diverse food web for microbes such as bacteria and protists. It has also been suggested that the bacterial assemblages within the phycosphere are species-specific and can vary depending on different environmental factors.
A phytobiome consists of a plant (phyto) situated in its specific ecological area (biome), including its environment and the associated communities of organisms which inhabit it. These organisms include all macro- and micro-organisms living in, on, or around the plant including bacteria, archaea, fungi, protists, insects, animals, and other plants. The environment includes the soil, air, and climate. Examples of ecological areas are fields, rangelands, forests. Knowledge of the interactions within a phytobiome can be used to create tools for agriculture, crop management, increased health, preservation, productivity, and sustainability of cropping and forest systems.
Induced Systemic Resistance (ISR) is a resistance mechanism in plants that is activated by infection. Its mode of action does not depend on direct killing or inhibition of the invading pathogen, but rather on increasing physical or chemical barrier of the host plant. Like the Systemic Acquired Resistance (SAR) a plant can develop defenses against an invader such as a pathogen or parasite if an infection takes place. In contrast to SAR which is triggered by the accumulation of salicylic acid, ISR instead relies on signal transduction pathways activated by jasmonate and ethylene.
Mycorrhiza helper bacteria (MHB) are a group of organisms that form symbiotic associations with both ectomycorrhiza and arbuscular mycorrhiza. MHBs are diverse and belong to a wide variety of bacterial phyla including both Gram-negative and Gram-positive bacteria. Some of the most common MHBs observed in studies belong to the phylas Pseudomonas and Streptomyces. MHBs have been seen to have extremely specific interactions with their fungal hosts at times, but this specificity is lost with plants. MHBs enhance mycorrhizal function, growth, nutrient uptake to the fungus and plant, improve soil conductance, aid against certain pathogens, and help promote defense mechanisms. These bacteria are naturally present in the soil, and form these complex interactions with fungi as plant root development starts to take shape. The mechanisms through which these interactions take shape are not well-understood and needs further study.
Plant root exudates are fluids emitted through the roots of plants. These secretion influence the rhizosphere around the roots to inhibit harmful microbes and promote the grow of self and kin plants.
The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a holobiont. Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments.
References
- 1 2 Weller, DM; Raaijmakers, JM; Gardener, BB; Thomashow, LS (2002). "Microbial populations responsible for specific soil suppressiveness to plant pathogens". Annual Review of Phytopathology. 40: 309–48. doi:10.1146/annurev.phyto.40.030402.110010. PMID 12147763.
- ↑ Babalola, O. O. (2010). Beneficial bacteria of agricultural importance. Biotechnology Letters, 32(11), 1559-1570. doi:10.1007/s10529-010-0347-0
- ↑ Terpolilli, J. J., Hood, G. A., & Poole, P. S. (2012). What determines the efficiency of N2-fixing Rhizobium-legume symbioses?. In Advances in microbial physiology (Vol. 60, pp. 325-389). Academic Press.
- ↑ Somers, E., Vanderleyden, J., & Srinivasan, M. (2004). Rhizosphere bacterial signalling: a love parade beneath our feet. Critical reviews in microbiology, 30(4), 205-240.
- ↑ Raaijmakers, J. M., Paulitz, T. C., Steinberg, C., Alabouvette, C., & Moënne-Loccoz, Y. (2009). The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant and soil, 321(1-2), 341-361.
- ↑ Lynch, J. M., & Whipps, J. M. (1990). Substrate flow in the rhizosphere. Plant and soil, 129(1), 1-10.
- ↑ Bakker, M. G., Chaparro, J. M., Manter, D. K., & Vivanco, J. M. (2015). Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays. Plant and Soil, 392(1-2), 115-126.
- ↑ Bakker, M. G., Manter, D. K., Sheflin, A. M., Weir, T. L., & Vivanco, J. M. (2012). Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant and Soil, 360(1-2), 1-13.
- ↑ Latz, E., Eisenhauer, N., Rall, B. C., Scheu, S., & Jousset, A. (2016). Unravelling linkages between plant community composition and the pathogen-suppressive potential of soils. Scientific reports, 6, 23584.
- ↑ Peters, R. D., Sturz, A. V., Carter, M. R., & Sanderson, J. B. (2003). Developing disease-suppressive soils through crop rotation and tillage management practices. Soil and Tillage Research, 72(2), 181-192.