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Soil microbes

Tao Song, Hui Xu, Congchong Wei, Tengfei Jiang, Shishang Qin, Weijia Zhang, Yu Cao, Chao Hu, Fan Zhang, Dairong Qiao, Yi Cao
Seaweed is receiving an increasing amount of attention as a "sea vegetable". The microbiota of coastal populations may acquire seaweed associated enzymes through marine food. Several agarases have been found in non-marine environments; however, their origin is unknown. In this study, a hypothetical protein, Aga1, was identified as an agarase from an inland soil agar-degrading bacterium, Paenibacillus sp. SSG-1.Having low similarity to known glycoside hydrolases, Aga1 may be a distant member of the glycoside hydrolase family 86...
October 19, 2016: Scientific Reports
Qing Fang, Zhengqiu Fan, Yujing Xie, Xiangrong Wang, Kun Li, Yafeng Liu
The quest for new, promising and indigenous plant growth-promoting rhizobacteria and a deeper understanding of their relationship with plants are important considerations in the improvement of phytoremediation. This study focuses on the screening of plant beneficial Cu/Zn-resistant strains and assessment of their bioremediation potential (metal solubilization/tolerance/biosorption and effects on growth of Brassica napus seedlings) to identify suitable rhizobacteria and examine their roles in microbes-assisted phytoremediation...
2016: Frontiers in Plant Science
Upendra Kumar, J Berliner, Totan Adak, Prakash C Rath, Avro Dey, Somnath S Pokhare, Nitiprasad N Jambhulkar, P Panneerselvam, Anjani Kumar, Shyamranjan D Mohapatra
Application of pesticide in agricultural fields is "unnecessary evil" for non-target microflora and fauna. Hence, to identify the safer pesticide molecules against non-target microbes, a long-term pesticide experiment was initiated at National Rice Research Institute, Cuttack, India. In the present study, the effect of continuous application of chlorpyrifos (0.5kgha(-1)) in rice fields on non-target groups of soil microbes and nematodes was studied for seven seasons (four wet and three dry seasons) during 2009-2013...
October 13, 2016: Ecotoxicology and Environmental Safety
Waheed Ullah Khan, Nasim Ahmad Yasin, Sajid Rashid Ahmad, Aamir Ali, Shakil Ahmed, Aqeel Ahmad
In our current study four nickel tolerant (Ni-tolerant) bacterial species viz: Bacillus thuringiensis 002, Bacillus fortis 162, Bacillus subtilis 174 and Bacillus farraginis 354 were screened by using Ni contaminated media. The screened microbes exhibited positive results for synthesis of indole acetic acid (IAA), siderophore production and phosphate solubilization. The effects of these screened microbes on Ni mobility in the soil, root elongation, plant biomass and Ni uptake in Althea rosea plants grown in Ni contaminated soil (200 mg Ni kg(-1)) were evaluated...
October 14, 2016: International Journal of Phytoremediation
Tasha M Santiago-Rodriguez, Raúl J Cano
Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity...
August 2016: Microbiology Spectrum
Susanne Kramer, Dörte Dibbern, Julia Moll, Maike Huenninghaus, Robert Koller, Dirk Krueger, Sven Marhan, Tim Urich, Tesfaye Wubet, Michael Bonkowski, François Buscot, Tillmann Lueders, Ellen Kandeler
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil...
2016: Frontiers in Microbiology
Yue Zhao, Jun Yao, Zhimin Yuan, Tianqi Wang, Yiyue Zhang, Fei Wang
Microbially induced carbonate precipitation (MICP) is an emerging and promising bioremediation technology to restore the environment polluted by heavy metals. Carbonate-biomineralization microbe can immobilize heavy metals from mobile species into stable crystals. In the present manuscript, laboratory batch studies were conducted to evaluate the Cd removal ability based on biosorption and MICP, using carbonate-biomineralization microbe GZ-22 isolated from a mine soil. This strain was identified as a Bacillus sp...
October 8, 2016: Environmental Science and Pollution Research International
Didier Bouchon, Martin Zimmer, Jessica Dittmer
Bacterial symbionts represent essential drivers of arthropod ecology and evolution, influencing host traits such as nutrition, reproduction, immunity, and speciation. However, the majority of work on arthropod microbiota has been conducted in insects and more studies in non-model species across different ecological niches will be needed to complete our understanding of host-microbiota interactions. In this review, we present terrestrial isopod crustaceans as an emerging model organism to investigate symbiotic associations with potential relevance to ecosystem functioning...
2016: Frontiers in Microbiology
Lorenzo Vergani, Francesca Mapelli, Elisabetta Zanardini, Elisa Terzaghi, Antonio Di Guardo, Cristiana Morosini, Giuseppe Raspa, Sara Borin
Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils...
October 5, 2016: Science of the Total Environment
Rafael José Marques Peixoto, Karla Rodrigues Miranda, Leandro Araujo Lobo, Alessandra Granato, Pedro de Carvalho Maalouf, Hugo Emiliano de Jesus, Caio T C C Rachid, Saulo Roni Moraes, Henrique Fragoso Dos Santos, Raquel Silva Peixoto, Alexandre Soares Rosado, Regina Maria Cavalcanti Pilotto Domingues
The Antarctic soil microbial community has a crucial role in the growth and stabilization of higher organisms, such as vascular plants. Analysis of the soil microbiota composition in that extreme environmental condition is crucial to understand the ecological importance and biotechnological potential. We evaluated the efficiency of isolation and abundance of strict anaerobes in the vascular plant Deschampsia antarctica rhizosphere collected in the Antarctic's Admiralty Bay and associated biodiversity to metabolic perspective and enzymatic activity...
October 5, 2016: Extremophiles: Life Under Extreme Conditions
Tingting Ma, Liqiang Zhou, Li 'ke Chen, Zhu Li, Longhua Wu, Peter Christie, Yongming Luo
Excessive use of antibiotics potentially threatens human health, agricultural production and soil phytoremediation. This arouses concern over the potential adverse effects of a commonly used antibiotic, oxytetracycline (OTC), on plants used for soil remediation and possible stimulation of antibiotic resistance genes in soils. A greenhouse experiment was conducted to investigate different rates (0, 1, 5, and 25 mg kg-1) and frequencies (one single high and daily low application) of OTC addition to soil on phytoremediation of a heavy metal contaminated soil by Sedum plumbizincicola and/or Medicago sativa (alfalfa)...
October 5, 2016: Journal of Agricultural and Food Chemistry
Haryun Kim, Hee-Sung Bae, K Ramesh Reddy, Andrew Ogram
River tributaries are ecologically important environments that function as sinks of inorganic nitrogen. To gain greater insight into the nitrogen cycle (N-cycle) in these environments, the distributions and activities of microbial populations involved in the N-cycle were studied in riparian and stream sediments of the Santa Fe River (SFR) tributaries located in northern Florida, USA. Riparian sediments were characterized by much higher organic matter content, and extracellular enzyme activities, including cellobiohydrolase, β-d-glucosidase, and phenol oxidase than stream sediments...
September 30, 2016: Water Research
Elise S Gornish, Noah Fierer, Albert Barberán
Understanding plant-microbe relationships can be important for developing management strategies for invasive plants, particularly when these relationships interact with underlying variables, such as habitat type and seedbank density, to mediate control efforts. In a field study located in California, USA, we investigated how soil microbial communities differ across the invasion front of Taeniatherum caput-medusae (medusahead), an annual grass that has rapidly invaded most of the western USA. Plots were installed in habitats where medusahead invasion is typically successful (open grassland) and typically not successful (oak woodland)...
2016: PloS One
Davide Francioli, Elke Schulz, Guillaume Lentendu, Tesfaye Wubet, François Buscot, Thomas Reitz
Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome...
2016: Frontiers in Microbiology
Qianhui Zu, Linghao Zhong, Ye Deng, Yu Shi, Baozhan Wang, Zhongjun Jia, Xiangui Lin, Youzhi Feng
Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR...
2016: Frontiers in Microbiology
Jafar Ali, Abdul Hameed, Safia Ahmed, Muhammad Ishtiaq Ali, Shama Zainab, Naeem Ali
Biological routes of synthesising metal nanoparticles (NPs) using microbes have been gaining much attention due to their low toxicity and eco-friendly nature. Pseudomonas aeruginosa JP2 isolated from metal contaminated soil was evaluated towards extracellular synthesis of silver NPs (AgNPs). Cell-free extract (24 h) of the bacterial isolate was reacted with AgNO3 for 24 h in order to fabricate AgNPs. Preliminary observations were recorded in terms of colour change of the reaction mixture from yellow to greyish black...
October 2016: IET Nanobiotechnology
Waseem Raza, Ning Ling, Dongyang Liu, Zhong Wei, Qiwei Huang, Qirong Shen
The volatile organic compounds (VOCs) produced by soil microbes have a significant role in the control of plant diseases and plant growth promotion. In this study, we examined the effect of VOCs produced by Pseudomonas fluorescens strain WR-1 on the growth and virulence traits of tomato wilt pathogen Ralstonia solanacearum. The VOCs produced by P. fluorescens WR-1 exhibited concentration dependent bacteriostatic effect on the growth of R. solanacearum on agar medium and in infested soil. The VOCs of P. fluorescens WR-1 also significantly inhibited the virulence traits of R...
November 2016: Microbiological Research
Olaya Rendueles, Gregory J Velicer
Evolutionary adaptation can be achieved by mechanisms accessible to all organisms, including faster growth and interference competition, but self-generated motility offers additional possibilities. We tested whether 55 populations of the bacterium Myxococcus xanthus that underwent selection for increased fitness at the leading edge of swarming colonies adapted by swarming faster toward unused resources or by other means. Populations adapted greatly but diversified markedly in both swarming phenotypes and apparent mechanisms of adaptation...
September 23, 2016: ISME Journal
Silvia Pajares, Ana E Escalante, Ana M Noguez, Felipe García-Oliva, Celeste Martínez-Piedragil, Silke S Cram, Luis Enrique Eguiarte, Valeria Souza
Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils...
2016: PeerJ
Yoshiaki Ueda, Katharina Frindte, Claudia Knief, Md Ashrafuzzaman, Michael Frei
Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated...
2016: PloS One
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