Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.

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Thermophilic and alkaliphilic Actinobacteria: biology and potential applications.

All the crops require nitrogen, phosphorus, and potassium macronutrients for proper plant growth, and addition of mineral fertilizers leads to impressive crop yield increases. Excessive application of chemical fertilizers increases the cost of crop production and causes environmental pollution. Many microorganisms inhabiting soil/rhizosphere play an important role in solubilization of bound form of soil minerals and enhance the availability of nutrients in the soil for plant growth and development. These plant growth-promoting rhizobacteria, including N2-fixing, phosphate-/potassium-solubilizing bacteria, are being used as biofertilizers to minimize health hazards caused by the use of chemical fertilizers. About 90–98 % of total potassium in soil exists in unavailable mineral form. Silicate minerals such as K-feldspars and biotite are the most common minerals in the Earth’s crust and are a source of inorganic nutrients in soils to provide optimal nutrition for crops. Recently, K-solubilizing bacteria/fungi have been isolated from rhizosphere soil of different crops, which cause potassium solubilization by production of organic/inorganic acids or by production of polysaccharides. Efficient K-solubilizing bacteria have been reported to enhance potassium uptake in plants leading to plant growth stimulation under pothouse and field conditions. These K-solubilizing bacteria (KSB) could be applied as potential biofertilizers along with application of rock K materials to provide a continuous supply of available potassium for increasing the crop yield.

Potassium-Solubilizing Microorganisms (KSMs) and Its Effect on Plant Growth Improvement

Phosphorus (P) availability is usually low in soils around the globe. Most soils have a deficiency of available P; if they are not fertilized, they will not be able to satisfy the P requirement of plants. P fertilization is generally recommended to manage soil P deficiency; however, the low efficacy of P fertilizers in acidic and in calcareous soils restricts P availability. Moreover, the overuse of P fertilizers is a cause of significant environmental concerns. However, the use of arbuscular mycorrhizal fungi (AMF), phosphate-solubilizing bacteria (PSB), and the addition of silicon (Si) are effective and economical ways to improve the availability and efficacy of P. In this review the contributions of Si, PSB, and AMF in improving the P availability is discussed. Based on what is known about them, the combined strategy of using Si along with AMF and PSB may be highly useful in improving the P availability and as a result, its uptake by plants compared to using either of them alone. A better understanding how the two microorganism groups and Si interact is crucial to preserving soil fertility and improving the economic and environmental sustainability of crop production in P deficient soils. This review summarizes and discusses the current knowledge concerning the interactions among AMF, PSB, and Si in enhancing P availability and its uptake by plants in sustainable agriculture.

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Contribution of Arbuscular Mycorrhizal Fungi, Phosphate–Solubilizing Bacteria, and Silicon to P Uptake by Plant

One of the main obstacles to plant growth is the lack of the availability of nutrient elements in many agricultural environments in the world, especially the tropics where soils can be extremely low in nutrients. Using different mechanisms of action, plant growth-promoting rhizobacteria (PGPR) participate in geochemical nutrition cycles and determine their access to plants and the microbial community of the soil. Use of these bacteria as bio-inoculants will increase the availability of nutrient elements in soil, help to minimize the chemical fertilizer application, reduce environmental pollution, and promote sustainable agriculture. Considering comprehensive reviews previously published on plant growth enhancement mechanisms, this review focuses on what is known about the action mechanisms underlying the increase of the availability of nutrient elements as an effect of microbial colonization especially PGPR. In this chapter, some of the most important mechanisms and processes regarding the effects of PGPR on the availability and hence uptake of nutrient elements by plant are reviewed. The awareness of such mechanisms can be important for the selection and hence production of microbial inoculums, which are appropriate for biological fertilization as substituting or decreasing the need of using chemical fertilizers in crops. In this review, special consideration is given to the role of PGPR in the availability of nitrogen (N), phosphorus (P), potassium (K), and sulfur (S) as macronutrients and iron (Fe) and manganese (Mn) as micronutrients.

Plant Growth-Promoting Rhizobacteria (PGPR) and Their Action Mechanisms in Availability of Nutrients to Plants

Increased biomass and quality and reduced heavy metal accumulation of edible tissues of vegetables in the presence of Cd-tolerant and immobilizing Bacillus megaterium H3.

The purposes of this study were to isolate and evaluate the interaction between mineral-weathering bacteria and silicate minerals (feldspar and biotite). A mineral-weathering bacterium was isolated from weathered rocks and identified as Rhizobium
 tropici Q34 based on 16S rRNA gene sequence analysis. Si and K concentrations were increased by 1.3- to 4.0-fold and 1.1- to 1.7-fold in the live bacterium-inoculated cultures compared with the controls respectively. Significant increases in the productions of tartaric and succinic acids and extracellular polysaccharides by strain Q34 were observed in cultures with minerals. Furthermore, significantly more tartaric acid and polysaccharide productions by strain Q34 were obtained in the presence of feldspar, while better growth and more citric acid production of strain Q34 were observed in the presence of biotite. Mineral dissolution experiments showed that the organic acids and polysaccharides produced by strain Q34 were also capable of promoting the release of Si and K from the minerals. The results showed that the growth and metabolite production of strain Q34 were enhanced in the presence of the minerals and different mineral exerted distinct impacts on the growth and metabolite production. The bio-weathering process is probably a synergistic action of organic acids and extracellular polysaccharides produced by the bacterium.

Isolation and the interaction between a mineral-weathering Rhizobium tropici Q34 and silicate minerals

Bacteria play important roles in mineral weathering, element mobilization, and soil formation. However, little is known about the mineral-weathering bacteria in subsurface soil environments. In this study, a total of 360 bacterial isolates were isolated from the different horizons of a soil profile and characterized for their mineral-weathering abilities and diversity along the soil profile. Among the 360 isolates, 226 isolates were found to have the ability to weather biotite. The average of released Fe, Si, and Al were significantly higher by the isolates from deeper horizons than from upper horizons. Although the proportion of the highly effective Fe solubilizers was not significantly different among the different horizons, the proportion of the highly effective Si and Al solubilizers was significantly higher in the deeper horizons than in the upper horizons. Furthermore, the element-releasing patterns of the mineral-weathering bacteria were different among the different horizons. Most of mineral-weathering bacteria from the soil profile could significantly lower the culture medium pH in the mineral-weathering process. The diversity of the mineral-weathering bacteria was higher in the upper horizons than in the deeper horizons. The weathering bacteria belonged to 12 bacterial genera, among which Burkholderia, Bacillus, and Lysinibacillus were the dominant and high-efficient weathering bacteria. The results showed the depth-related changes in the weathering capacity and community structures of the culturable mineral-weathering bacteria and suggested the possible roles of the bacteria in the mineral-weathering and element mobilization along the soil profile.

Changes in weathering effectiveness and community of culturable mineral-weathering bacteria along a soil profile

Microorganisms play important role in mineral weathering. However, little is known about rock-associated mineral-dissolving bacteria. In this study, 129 bacterial isolates were obtained from the less and more weathered mica schist surfaces and the adjacent soil and characterized for mineral dissolving activity, population, and the linkage of rock weathering level and distribution of the bacteria. Among the 129 isolates, 112 isolates could dissolve biotite. The relative abundance of the highly effective Fe solubilizers was significantly higher on the more altered rock surface (89.6%) than in the soil (51.2%) and on the less altered rock surface (22.5%), while the relative abundance of the highly effective Si solubilizers was significantly higher in the soil (65.9%) than on the more (41.7%) and less (12.5%) altered rock surfaces. Furthermore, 17.5-42.5%, 87.5%, and 60.9-90.2% of the highly effective acid- and siderophore-producing isolates were obtained in the less and more weathered rocks and the soil, respectively. The mineral-dissolving bacteria belonged to 18 genera and Burkholderia, Bacillus, and Paenibacillus were the dominant and highly effective mineral-dissolving bacteria. Phylogenetic analysis found 2, 9, and 5 bacterial species in the highly effective mineral-dissolving bacteria on the less and more altered rock surfaces and in the soil, respectively. The results showed the abundant and diverse mineral-dissolving bacterial populations on the more weathered rock surfaces. The results also suggested distinct mineral-dissolving activities and mechanisms of the bacteria and highlighted the possibility for the development of bacterial inocula for plant nutrition improvement in silicate mineral-rich soils.

Isolation and characterization of mineral-dissolving bacteria from different levels of altered mica schist surfaces and the adjacent soil

A Gram-stain-positive, non-motile, rod- or coccoid-shaped actinobacterium, designated strain A33T, was isolated from a forest soil sample from Nanjing, Jiangsu Province, PR China. The strain grew optimally at 30 °C, pH 7.0 and with 3 % NaCl (w/v). Phylogenetic analysis of the strain, based on 16S rRNA gene sequences, showed that it was most closely related to 
Arthrobacter woluwensis
(98.4 % sequence similarity), 
Arthrobacter humicola
(97.5 %), 
Arthrobacter globiformis
(97.4 %), 
Arthrobacter oryzae
(97.3 %) and 
Arthrobacter cupressi
(97.0 %). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0; MK-9(H2) was the predominant respiratory quinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and three glycolipids. Cell-wall analysis revealed that the peptidoglycan type was A3α, based on l-lysine-l-alanine; the cell-wall sugars were galactose and mannose. The genomic G+C content of strain A33T was 66.8 mol%. The low DNA–DNA relatedness values between strain A33T and recognized species of the genus 
Arthrobacter
and many phenotypic properties supported the classification of strain A33T as a representative of a novel species of the genus 
Arthrobacter
, for which the name Arthrobacter nanjingensis sp. nov. is proposed. The type strain is A33T ( = CCTCC AB 2014069T = DSM 28237T).

Arthrobacter nanjingensis sp. nov., a mineral-weathering bacterium isolated from forest soil.

A hydroponic culture experiment was performed to investigate the effects of endophytic Bacillus megaterium H3 on the plant biomass, Cd accumulation and tolerance of hybrid pennisetum, and the mechanisms involved in the different levels of Cd-contaminated aquatic environments. Strain H3 significantly increased the plant growth (ranging from 13 to 71 %) and total Cd uptake (ranging from 41 to 160 %) but decreased Cd translocation factors of hybrid pennisetum treated with 0-20 μM Cd compared with the controls. Furthermore, most of Cd (71-77 %) was accumulated in the roots of the bacterial-inoculated hybrid pennisetum. Notably, strain H3 could significantly increase the production of oxalic and propanedioic acids (ranging from 18 to 188 %) but decrease the production of phytochelatins of hybrid pennisetum compared to the controls under different levels of Cd stress. The live bacterial-induced increase in organic acid production and decrease in phytochelatins production by hybrid pennisetum might be responsible for the increased plant growth, root Cd accumulation, and Cd toxicity alleviation of the plant under different levels of Cd stress. The results highlight that hybrid pennisetum plus endophytic B. megaterium H3 may be utilized for biomass production and Cd phytostabilization of the plant in the different levels of Cd-contaminated aquatic environments.

Inoculation with endophytic Bacillus megaterium H3 increases Cd phytostabilization and alleviates Cd toxicity to hybrid pennisetum in Cd-contaminated aquatic environments

Lin Yan He

Papers

Isolation and the interaction between a mineral-weathering Rhizobium tropici Q34 and silicate minerals

Changes in weathering effectiveness and community of culturable mineral-weathering bacteria along a soil profile

Isolation and characterization of mineral-dissolving bacteria from different levels of altered mica schist surfaces and the adjacent soil

Arthrobacter nanjingensis sp. nov., a mineral-weathering bacterium isolated from forest soil.

Inoculation with endophytic Bacillus megaterium H3 increases Cd phytostabilization and alleviates Cd toxicity to hybrid pennisetum in Cd-contaminated aquatic environments