Soil sampling based on field spatial variability of soil microbial indicators

2009 ◽  
Vol 45 (5-6) ◽  
pp. 488-495 ◽  
Author(s):  
Joséphine Peigné ◽  
Jean-François Vian ◽  
Mario Cannavacciuolo ◽  
B. Bottollier ◽  
Rémi Chaussod
Pedosphere ◽  
2011 ◽  
Vol 21 (2) ◽  
pp. 207-213 ◽  
Author(s):  
Dong-Sheng YU ◽  
Zhong-Qi ZHANG ◽  
Hao YANG ◽  
Xue-Zheng SHI ◽  
Man-Zhi TAN ◽  
...  

Author(s):  
Carolina Grings Serafini ◽  
Naiara Jacinta Clerici ◽  
Isabela Karina Della-Flora ◽  
Gabriele Kuhn Dupont ◽  
Liziara da Costa Cabrera ◽  
...  

2019 ◽  
Vol 11 (3) ◽  
pp. 862 ◽  
Author(s):  
Abhishek Kumar ◽  
Rajiv Rakshit ◽  
Arnab Bhowmik ◽  
Nintu Mandal ◽  
Anupam Das ◽  
...  

Modern agricultural innovations with nanomaterials are now being applied in every sphere of agriculture. However, their interaction with soil microbial processes is not being explored in detail. This initiative was undertaken to understand the effect of metal-oxide nanoparticles with heat stress in soil. Metal-oxide nanoparticles, zinc oxide (ZnO), and iron oxide (Fe2O3) (each at 10 and 40 mg kg−1 w/w) were mixed into uncontaminated soil and subjected to heat stress of 48 °C for 24 hours to assess their effect on soil biological indicators. The resistance indices for the acid (ACP), alkaline phosphatase (AKP) activity, and fluorescein diacetate hydrolyzing (FDA) activity (0.58 to 0.73, 0.58 to 0.66, and 0.42 to 0.48, respectively) were higher in the presence of ZnO nanoparticles as compared to Fe2O3 nanomaterials, following an unpredictable pattern at either 10 or 40 mg kg−1 in soils, except dehydrogenase activity (DHA), for which the activity did not change with ZnO nanomaterial. An explicit role of ZnO nanomaterial in the revival pattern of the enzymes was observed (0.20 for DHA, 0.39 for ACP, and 0.43 for AKP), except FDA, which showed comparable values with Fe2O3 nanomaterials for the following 90 day (d) after stress. Microbial count exhibiting higher resistance values were associated with Fe2O3 nanoparticles as compared to ZnO nanomaterials, except Pseudomonas. The recovery indices for the microbial counts were higher with the application of Fe2O3 nanomaterials (0.34 for Actinobacteria, 0.38 for fungi, 0.33 for Pseudomonas and 0.28 for Azotobacter). Our study emphasizes the fact that sensitive microbial indicators in soil might be hampered by external stress initially but do have the competency to recover with time, thereby reinstating the resistance and resilience of soil systems.


2016 ◽  
Vol 79 (7) ◽  
pp. 1197-1209 ◽  
Author(s):  
NORMA HEREDIA ◽  
CINDY CABALLERO ◽  
CARMEN CÁRDENAS ◽  
KARINA MOLINA ◽  
RAFAEL GARCÍA ◽  
...  

ABSTRACT To compare microbiological indicator and pathogen contamination among different types of fresh produce and environmental samples along the production chain, 636 samples of produce (rinsates from cantaloupe melons, jalapeño peppers, and tomatoes) and environmental samples (rinsates from hands of workers, soil, and water) were collected at four successive steps in the production process (from the field before harvest through the packing facility) on 11 farms in northern Mexico during 2011 and 2012. Samples were assayed for enteric pathogens (Escherichia coli O157:H7, other Shiga toxigenic E. coli, Salmonella, and Listeria monocytogenes) and microbial indicators (coliforms, other E. coli strains, and Enterococcus spp.). Salmonella was the only pathogen detected; it was found in one preharvest jalapeño sample (detection limits: 0.0033 CFU/ml in produce and hand samples, 0.0013 CFU/ml in water, and 0.04 CFU/g in soil). Microbial indicator profiles for produce, worker hands, and soil from jalapeño and tomato farms were similar, but cantaloupe farm samples had higher indicator levels (P < 0.05 for all comparisons) on fruit (6.5, 2.8, and 7.2 log CFU per fruit) and hands (6.6, 3.1, and 7.1 log CFU per hand) for coliforms, E. coli, and Enterococcus, respectively, and lower E. coli levels in soil (<1 CFU/g). In water from tomato farms, E. coli indicators were significantly more prevalent (70 to 89% of samples were positive; P = 0.01 to 0.02), and geometric mean levels were higher (0.3 to 0.6 log CFU/100 ml) than those in cantaloupe farm water (32 to 38% of samples were positive, geometric mean <1 CFU/100 ml). Microbial indicators were present during all production steps, but prevalence and levels were generally highest at the final on-farm production step (the packing facility) (P < 0.03 for significant comparisons). The finding that microbial contamination on produce farms is influenced by produce type and production step can inform the design of effective approaches to mitigate microbial contamination.


mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland‐Moritz ◽  
Tess E. Brewer ◽  
...  

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.


2020 ◽  
Vol 117 (13) ◽  
pp. 7263-7270 ◽  
Author(s):  
Kelly Gravuer ◽  
Anu Eskelinen ◽  
Joy B. Winbourne ◽  
Susan P. Harrison

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.


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