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Maps and sampling strategy/land use types: non-tilled vineyard (NV), cork oak forest (CO), pasture (PA), hay crop (HC) and tilled vineyard (TV).
Source publication
To evaluate the effects of management practices and seasons on a soil bacterial community and the composition of ammonia-oxidizing bacteria (AOB), molecular screenings were compared among Mediterranean (Sardinia) soils with different plant covers and different agricultural practices, namely cork oak forest, tilled/non-tilled vineyard, hay crop and...
Context in source publication
Citations
... On the other hand, the distinct seasonal variability in the TOC/peak A fluorescence intensity ratio in soil waters (Fig. 4) could be a consequence of the increased activity of the edaphic microbial community (bacteria, fungi, actinomycetes, among others) during the springtime, producing more humic and fulvic acids (Francioli et al., 2014;Barnard et al., 2015). The coefficient of variation of peak A decreases by 40% between 30 and 60 cm deep in the spring season. ...
... In our study, a key effect associated with soil disturbance was the disruption of ERM and the loss of a particular habitat for many soil microbes, specifically P solubilizers, in addition with a great decrease in MBC and dehydrogenase activity. Many studies have shown that the tillage decreases the soil microbial biomass and enzymatic activity (Adetunji et al., 2017;Francioli et al., 2014;Laudicina et al., 2011;Madejón et al., 2009;Martin-Lammerding et al., 2013;Vazquez et al., 2017). ...
In cropping systems, the choices adopted for the tillage system used and plants cultivated can strongly influence the soil microbial population and its functional profile. Arbuscular mycorrhizal fungi (AMF) are an important component of soil microbiome and their mutualistic symbiosis with the majority of higher plants grant the latter a wide range of benefits. The extraradical mycelium (ERM) developed by these fungi expands the volume of soil influenced and harbors a diversity of microbes establishing a distinct environment of complementary interactions. We assessed how growing plants with different levels of mycotrophy modifies the biological activity profile in the soil under Mn toxicity and whether this is modified by soil disturbance. Following mycotrophic plants, soil contained a more active microbiome than after the non‐mycotrophic plants, as expressed by higher values of soil basal respiration or dehydrogenase activity. Additionally, the count of phosphorus solubilizes and activity of phosphatase were greater after mycotrophic plants. Even among mycotrophic plants, different profiles of biological activity can be distinguished after growing a legume or grass. ERM disruption by soil disturbance decreased most of the parameters studied and for phosphatase activity and P solubilizers in a more significant way. These results indicate that even under Mn toxicity, the microbiome associated with AMF symbiosis following mycotrophic plants growth presented a higher biological activity and had a differential biological response towards the stress imposed by soil disturbance, when compared to the microbiome associated with non‐mycotrophic roots.
... Temporal heterogeneity is measured based on inter-annual variability (Costello and Daane 2003;Thomson and Hoffmann 2007;Smith and Bettiga 2008;Okur et al. 2009;Baumgartner et al. 2010;Kruger et al. 2015;Gagnarli et al. 2015;Costantini et al. 2015;Laudicina et al. 2017;Rodríguez-Salgado et al. 2017;Simoni et al. 2018;Canfora et al. 2018;Chou et al. 2018;Berlanas et al. 2019), seasonal variability (Renaud et al. 2004;Thomson and Hoffmann 2007;Steenwerth and Belina 2008a, b;Pérez-Bote and Romero 2012;López-Piñeiro et al. 2013;Francioli et al. 2014;Bevivino et al. 2014;Chou et al. 2018;Vega-ávila et al. 2018;Hernandez and Menéndez 2019;Berlanas et al. 2019), the effects of grapevine age (Costantini et al. 2015;Manici et al. 2017) and of the time since conversion to organic production (Coll et al. 2011Likar et al. 2017;Van Geel et al. 2017). All the soil biological quality parameters appear to vary across seasons and years. ...
Viticulture is a key sector of the agricultural economy of the main wine-producing countries, e.g. Italy, France, Spain and the USA, but is also one of the main users of phytosanitary products and mechanization. Over the last 15 years, numerous studies of the effect of viticultural practices on soil quality have evidenced strong impacts on soil physical, chemical and biological quality. However, to date a global analysis providing a comprehensive overview of the ecotoxicological impacts of viticultural practices on soil biological quality is missing. Here, we conducted a meta-analysis of the literature in order to rank viticultural production systems and practices according to their impact on soil biodiversity and functioning in the context of the agro-ecological transition. We screened about one hundred articles and gathered data on more than 50 viticultural factors and 230 soil biological parameters. The results show that soil microorganisms are threefold to fourfold higher under organic viticulture than under conventional viticulture in terms of biomass, respiration and activity; and that biodynamic viticulture shows a similar trend than organic viticulture. Tillage, the absence of soil cover and mineral fertilization are significantly deleterious to the whole soil biodiversity, whereas cover crops, organic fertilizers and addition of grapevine pruning wood are beneficial. Pesticides—especially herbicides—have an ecotoxicological impact on soil organisms, notably on nematodes with losses of up to two-thirds of individuals. The pivotal role of biodiversity in soil functions implies that this degradation will have substantial consequences on the ecological and agronomical services provided by the soil for vine production. On this basis, we propose a potentially more agro-ecological and sustainable vine production system based on the more virtuous practices.
... A study conducted by Cleary et al. (2012) emphasised the advantages of DGGE over barcoded pyrosequencing, with the former providing a relatively rapid and economic means of exploring variations in the community composition. The universal primers used in the present study (968F/1401R) for DGGE have been popularly used by researchers (Yong et al. 2011;Francioli et al. 2014;Kutvonen et al. 2015). Several studies have claimed that the primer pair 968F/1401R has the ability to resolve environmental samples better as compared to other primers used for DGGE (Xing et al. 2006;Peng et al. 2007;Wei et al. 2008;Ccoscco et al. 2018). ...
The present study is an attempt to understand the impact of bioinoculants, Azotobacter chroococcum (A), Bacillus megaterium (B), Pseudomonas fluorescens (P), on (a) soil and plant nutrient status, (b) total resident and active bacterial communities, and (c) genes and transcripts involved in nitrogen cycle, during cultivation of Cajanus cajan. In terms of available macro- and micro-nutrients, triple inoculation of the bioinoculants (ABP) competed well with chemical fertilizer (CF). Their ‘non-target’ effects were assessed in terms of the abundance and activity of the resident bacterial community by employing denaturing gradient gel electrophoresis (DGGE). The resident bacterial community (16S rRNA gene) was stable, while the active fraction (16S rRNA transcripts) was influenced (in terms of abundance) by the treatments. Quantification of the genes and transcripts involved in N cycle by qPCR revealed an increase in the transcripts of nifH in the soil treated with ABP over CF, with an enhancement of 3.36- and 1.57- fold at flowering and maturity stages of plant growth, respectively. The bioinoculants shaped the resident microflora towards a more beneficial community, which helped in increasing soil N turnover and hence, soil fertility as a whole.
... Most studies of microbial and other soil properties are focused on the differences in their spatial structure that are caused by natural and anthropogenic factors. It was shown that the spatial distribution of soil microorganisms depends on the position in landscape (Du et al. 2015), type of land use (e.g., forest vs. cultivated field) (Francioli et al. 2014), time and methods of soil sampling, and soil treatment (e.g., different types of tillage, fertilization, or crop rotation) (Garcia-Orenes et al. 2013). ...
Purpose
Knowledge about the spatio-temporal variability of soil microbial properties is crucial in evaluating their structure-function relationship and their impact on ecosystem functions. The aim of the study was to determine the spatio-temporal variation of the selected microbial properties at the surface horizon in a conventionally managed arable field.
Materials and methods
The area selected for the research, which was mainly covered with typical Luvisols, was a uniformly managed system that was considered to be homogenous in respect to texture (mostly loamy fine sand). Winter wheat was cultivated after winter rape as the forecrop. A grid soil sampling (10 m × 10 m) was used to assess the spatial heterogeneity of soil properties across a 0.5-ha field. Soil samples were collected at 50 points from the upper 20 cm of soil in April and August 2007. Colony-forming units (CFUs) of bacteria, fungi and actinomycetes, and basal respiration (BR) were analyzed. Data were evaluated using classical statistical and geostatistical methods.
Results and discussion
Fungal CFUs were significantly lower than the bacterial ones with a B/F (bacteria/fungi) ratio of 80.0 in April and 45.1 in August. Bacterial CFUs, B/F ratio, and BR level revealed significantly higher values in April than in August, while fungi showed the opposite trend. Other studied properties did not show significant differences between sampling months. Only some of the properties, such as the bacterial community in August, the number of actinomycetes in April, and qCO2 on both sampling dates, revealed significant spatial autocorrelation (Moran’s I) and were spatially dependent at the scale of sampling grid, whereas the qCO2 revealed a higher differentiation in the spatial pattern between April and August than the other studied properties. Most of the spatially correlated properties were in the weak variability class (a nugget effect > 75%), while only the qCO2 (August) ratio was in the moderate variability class (a nugget effect between 25 and 75%).
Conclusions
Most of the microbial-related properties did not exhibit a spatial structure at the examined scale, thus suggesting that changes in these properties would be detectable at a distance shorter than 10 m. More frequent seasonal sampling must be included in the sampling strategy in order to better understand whether studied properties show any permanent spatial patterns in soil over time or whether they are more randomized.
... The characterisation of bacterial communities in Mediterranean cork oak ecosystems has been poorly investigated compared to mycorrhizal communities. The predominance of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phyla has been reported (Lagomarsino et al., 2011;Bevivino et al., 2014), but the majority of studies focused on global response of soil microbial activity to land use practices (Marongiu et al., 2006;Lagomarsino et al., 2011;Costa et al., 2013;Francioli et al., 2014). A functional group was particularly investigated, the soil denitrifying bacteria. ...
... The assessment of soil microbial functionalities demonstrated a correlation among microbial activity, functional biodiversity and land use intensities. Soils subjected to low land use intensities showed a higher stability of bacterial communities and microbial activities compared to strong land use intensities (Lagomarsino et al., 2011;Bevivino et al., 2014), but as for EcM community, land use impacts are dependent on seasonal variations (Costa et al., 2013;Francioli et al., 2014;Bevivino et al., 2014). Biological invasion was also shown as a strong factor affecting soil microbial functional diversity in cork oak ecosystems (Boudiaf et al., 2013), as well as Q. suber seedlings. ...
Cork oak (Quercus suber L.) is an emblematic component of western Mediterranean basin landscapes. Cork oak forests have always been highly appreciated by local populations for their great ecological and socio-economic value. However, the sustainability of cork oak forests has been threatened in recent decades by a complex phenomenon of degradation called “oak decline”, worsened by the increase of anthropogenic and climatic disturbances combined with a lack or scarcity of natural cork oak regeneration. All these disturbances disrupt key components of the ecosystem, notably the rhizosphere microbiome, potentially sharpening decline processes and forest ecosystem degradation in return. This review provides an overview of the main abiotic and biotic decline drivers and a comprehensive state of knowledge about the impact of decline-related cork oak forest degradation on rhizosphere microbiome in Mediterranean basin. Finally, perspectives for the improvement of cork oak forest sustainability through the development of ecological management strategies based on rhizosphere microbiome-driven plant managements are highlighted.
... The increase in dsDNA recorded in the M in comparison with BS and BR treatments in the unfertilized treatments could indicate that the M treatment increased the amount of SOM which serves as the major energy and carbon source for microorganisms (Neumann et al., 2013). The average dsDNA measured in the unfertilized (12.32 µg g -1 ) plots was substantially higher than that measured by Franciolia et al. (2014) in a 30 year old pasture (7.2 µg g -1 ). According to Wallis et al. (2010), the main factor limiting microorganisms under burned sugarcane is probably the shortage of available carbon leading to the growth of communities able to use recalcitrant humic substances. ...
Under sugarcane production, soil aggregate stability (AS) is affected by the harvesting method i.e., burning, mulching and fertilizer application. This study combined mineralogical, biological, chemical and physical approaches to investigate the effect of these management techniques on a range of soil properties that may influence soil aggregation. The study site was located at the South African Sugarcane Research Institute (SASRI) at Mount Edgecombe near Durban, KwaZulu-Natal, South Africa. It is the oldest long-term, continuously monitored sugarcane production and soil management trial in the world, having been established in 1939. The area is characterized by summer (October to March) rainfall. Within the study site itself the dominant parent material was dolerite, with colluvial material in the south-western part of the lower slope. Due to the variation in topography, two soil types were identified. On the upper slope, the soil was classified as a Mollic Cambisol, locally known as Mayo form (Glenecho family). On the lower slope, the soil was a Mollic Nitisol, locally known as Bonheim form (Rockvale family). The trial is a split-plot factorial design arranged in a randomised complete block with four replicates for plots burned at harvest and eight replicates for all unburned plots. The main plot treatments are a) green sugarcane harvesting with all residues retained and spread evenly over the plot area (M), b) sugarcane burned prior to harvest (no foliage residue) with sugarcane-tops left scattered evenly over the plot area (BS) and c) sugarcane burned prior to harvest with all residue (sugarcane-tops) removed from the plots (BR). Split-plot treatments consisted of unfertilized (F0) and fertilized plots (F) receiving an annual application of 140 kg N, 28 kg P and 140 kg K ha-1 as 5:1:5 (46). From the 32 plots, 24 were selected including four replicates of each of the treatments.
Three replicate soil samples were collected with a spade at two soil depths (0-10 and 10-20 cm) from mini-pits in each of the 24 chosen plots. For soil AS determinations, samples were air-dried and sieved to collect soil aggregates between 2.8 and 5 mm and the mean weight diameter (MWD) determined. Some of the air-dried bulk sample was analysed for total carbon (Ct) and nitrogen (N), organic carbon (OC), pH, exchangeable calcium (Ca), magnesium (Mg), sodium (Na) and potassium (K), aluminium (Al), soil texture (clay, silt and sand content), clay mineralogy, soil microbiological properties, phosphorus (P), zinc (Zn), copper (Cu), and manganese (Mn). Soil microbiological properties (the abundance and communities of bacteria and fungi) were measured on the 0-10 cm depth samples only. The saturated hydraulic conductivity (Ks), bulk density (ρb), water retention and available water capacity (AWC) were determined on undisturbed soil cores also collected from 0-10 and 10-20 cm soil depths.
Penetrometer resistance (PR) and apparent electrical resistance were measured in-field across the whole trial while the gravimetric soil moisture was measured in the laboratory and then mapped for the whole trial.
Mulching and burning as well as fertilizer application showed no clear relationship with the clay mineralogy of the investigated soils. The main clay minerals in both soils were high defect kaolinite, vermiculite and lepidocrocite. The main difference in mineralogy found was that the upper slope soil also contained talc, illite and interstratified vermiculite-smectite which were not present in the lower slope soil. However, differences in clay mineralogy between the two slope positions had no influence on the other measured soil properties. The OC and Ct increased non-significantly (p > 0.05) in M and BS compared to BR in both fertilized and unfertilized treatments suggesting that the soils might have reached their equilibrium in terms of carbon. A significant increase (p < 0.05) caused by M treatment was, however, observed in N. The Ct and N were generally significantly higher (p < 0.05) in the macroaggregates compared to the microaggregates (0.1 - 0.05 mm) in most treatments, showing the direct contribution of soil organic matter (SOM) to the stability of larger aggregates.
The Ca, Mg, pH and effective cation exchange capacity (ECEC) of the soils were similar between burned (BR and BS) and mulched (M) treatments but they decreased significantly (p < 0.05) in the fertilized treatments. Sodium concentrations were higher in the BRF0 and BSF0 treatments compared to the rest of the treatments. Potassium was significantly higher (p < 0.05) in MF0, and MF treatments compared to BSF0 and BRF0 treatments. The decrease in soil pH was mirrored by an increase in Al concentration and acid saturation in the fertilized treatments. These results could be due to the combined effects of basic cation mining by sugarcane plants, leaching of basic cations and their replacement by Al, mineralization of mulch leading to soil acidification, and oxidization of ammonium to nitrate. The higher concentration of P in the M treatments suggested that P resulted from both the fertilizer application and mineralization of SOM. High K accumulation came from the annual NPK fertilizer application.
The dsDNA significantly increased (p < 0.05) in M compared to BR in the F0 treatments and remained similar between M, BS and BR treatments in the F treatments. It decreased significantly (p < 0.05) in the F compared to the F0 treatments. Although fertilizer application had no effect, M treatment significantly (p < 0.05) increased the abundance of bacteria and decreased the abundance of fungi 16S rDNA copy numbers. Bacterial richness significantly (p < 0.01) increased and decreased under mulching and fertilization, respectively, while the evenness decreased significantly (p < 0.01) in M and fertilized plots. Fungal richness significantly (p < 0.01) increased under M treatment in F0 treatments but showed no clear trend in the F treatments. Fertilizer application significantly (p < 0.01) reduced fungal richness. Burning and mulching showed no significant (p > 0.05) effect on fungal evenness though it was significantly (p < 0.01) decreased by fertilizer application. The MWD increased slightly in the following order: BR < BS < M under F treatments at the 0-10 cm depth, but the differences were not significant (p > 0.05). These results were associated with the lack of differences or consistent increase in soil aggregating agents observed between M and burned (BR and BS) treatments. The MWD was significantly (p < 0.05) reduced by fertilizer application possibly due to the decrease in divalent exchangeable bases (Ca and Mg) and fungal richness observed in this treatment compared to the F0 treatments. In the absence of a correlation between OC and MWD, the multivariate analyses showed that fungi were the main factor influencing AS though some significant effects of exchangeable bases were also found. The changes in MWD possibly induced by fertilizer application showed no effect on PR and the decrease in PR observed in the M treatments was attributed to an increase in moisture (due to higher SOM) compared to the burned treatments. Similarly to PR, bulk density, water retention and AWC showed no clear relationship with MWD. Therefore, the higher water retention found in BS and M treatments was attributed to the direct effect of SOM. The saturated hydraulic conductivity (Ks) decreased significantly (p < 0.05) in the fertilized treatments following the decrease in MWD. In conclusion, the long-term effect of mulching and burning on soil properties can be influenced by other external factors. In this study, the annual application of NPK fertilizer counteracted the impact of burning and mulching on AS and associated properties. Some of the properties were mostly influenced by soil type rather than sugarcane management practices. The annual application of NPK fertilizer also appeared to have led to increased acidification and soil structural deterioration (lower AS) under long-term sugarcane production regardless of the harvesting method practiced. Increasing additions of sugarcane residues are thus not necessarily sufficient to lead to improved soil structural stability and related soil properties.
... The characterisation of bacterial communities in Mediterranean cork oak ecosystems has been poorly investigated compared to mycorrhizal communities. The predominance of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phyla have been reported (Lagomarsino et al., 2011;Bevivino et al., 2014), but the majority of studies focused on global response of soil microbial activity to land use practices (Marongiu et al., 2006;Lagomarsino et al., 2011;Costa et al., 2013;Francioli et al., 2014). A functional group was particularly investigated, the soil denitrifying bacteria. ...
... The assessment of soil microbial functionalities demonstrated a correlation among microbial activity, functional biodiversity and land use intensities. Soils subjected to low land use intensities showed a higher stability of bacterial communities and microbial activities compare to strong land use intensities (Lagomarsino et al., 2011;Bevivino et al., 2014), but as for EcM community, land use impacts are dependant of seasonal variations (Costa et al., 2013;Francioli et al., 2014;Bevivino et al., 2014). Biological invasion was also shown as a strong factor affecting soil microbial functional diversity in cork oak ecosystems (Boudiaf et al., 2013), as well as Q. suber seedlings. ...
Le chêne-liège (Quercus suber) est une essence forestière d’une grande importance écologique et socio-économique pour les habitants de Méditerranée. Cependant, au cours des dernières décennies, ces subéraies et particulièrement les subéraies marocaines ont été soumises à de fortes contraintes climatiques, environnementales et humaines entrainant une accélération des processus de dégradation. La conservation de ces écosystèmes est fortement dépendante de notre capacité à prédire les changements induits par ces différentes pressions ainsi que du développement d’approches durables pour leur réhabilitation. Dans ce contexte, l’identification d’indicateurs biologiques de l’état de santé des subéraies et l'intensification des processus de facilitation entre plantes (arbres/arbustes) apparaissent comme des stratégies écologiques prometteuses. Le succès de ces approches est cependant assujetti à notre compréhension des interactions entre les communautés végétales et les champignons du sol, notamment les champignons mycorhiziens, éléments clés du fonctionnement des écosystèmes forestiers. Ce travail a visé le décryptage des réseaux fongiques, notamment mycorhiziens associés au chêne-liège et la végétation du sous-bois dans trois subéraies marocaines (Maâmora, Benslimane, Chefchaoun) caractérisées par différents niveaux de dégradation. La diversité fongique associée aux racines du chêne-liège et à plusieurs plantes arbustives représentatives des subéraies (Cistus salviifolius, Cistus monpeliensis et Lavandula stoechas) a été étudiée en combinant les méthodes traditionnelles basées sur l’aspect morphologique des mycorhizes et les nouvelles technologies de séquençage haut-débit par identification moléculaire des communautés fongiques.Les résultats obtenus représentent la plus vaste enquête de la diversité fongique du sol, notamment mycorhizienne, au sein des subéraies marocaines. Différents niveaux de structuration des communautés de champignons du sol ont été révélés, fonction de l’habitat, du type de plantes et de l'état de dégradation. Une large gamme d’indicateurs fongiques de l’état de dégradation de la subéraie, en lien avec la plantes hôte, ont pu être mise en évidence au sein des différents habitats, soulignant l’importance de plusieurs champignons ectomycorhiziens (notamment Cenococcum, Russula, Terfezia et Tomentella) mais aussi des champignons mycorhiziens éricoïdes (Cladophialophora, Oidiodendron) et à arbuscules (Rhizophagus, Redeckera, Racocetra, Paraglomus). Ce travail a permis d’établir une base de données majeure sur l’écologie des champignons du sol dans les subéraies marocaines, et de proposer un nouvel éclairage sur leur potentiel pour le suivi de l’état de santé des subéraies, ainsi que pour la mise en place de programmes de conservation adaptés tenant compte aussi des champignons associés. L’application des approches proposées à une plus large diversité d’écosystèmes forestiers devrait constituer un atout important pour la meilleure compréhension du fonctionnement biologique des écosystèmes forestiers et leur sauvegarde face à l’aggravation des pressions humaines et climatiques au niveau mondial.
... The dynamics of the bacterial community from all soil types were ranked as follows: spring 2012 (164.8 x 10 6 CFU g -1 ) > spring 2013 (147.7 x 10 6 CFU g -1 ) > autumn 2012 (80.6 x 10 6 CFU g -1 ) > autumn 2013 (79.4 x 10 6 CFU g -1 ). These results are in line with the previous studies and the favourable conditions (temperature, soil moisture) during spring (Bouskill et al., 2013;Francioli et al., 2014;Noe et al., 2012;Valverde et al., 2014) account for them. The recorded data showed significant seasonal variations (spring vs. autumn), for both years (p<0.05). ...
... The obtained results showed that in the same soil type the bacterial community was not only season dependent, as it was also affected by the way in which the land was farmed and managed (p<0.05). Similar to the present results, Francioli et al. (2014) reported that different land usages and seasons strongly influenced the dynamics and the composition of the bacterial community. ...
... Our findings about different land use and soil management practices (conventional, organic, and unmanaged) showed that during the four-season time span of our study, the bacterial richness, assessed through the plate counting method, was ranked as follows: hay crop > vegetable crop > hardwood forest > arable land under crop rotation > permanent grassland >vineyards. Recently, Francioli et al. (2014) reported similar results. The undisturbed forest soil (F) showed a higher bacterial content in comparison to managed soils (A, TV, VC, HC). ...
To evaluate the effects of seasonal fluctuations, soil types, land use and management inputs on the abundance and composition of soil bacteria, twenty soils types from Moldavia region located in north-eastern Romania were compared. Changes in soil microbiota are an early and sensitive indicator of soil pollution and can be used to predict long-term trends in soil quality. The use of microbial properties as indicator of soil pollution is easily measured and can also be measured accurately across a wide range of soil types and conditions. The dynamics of the bacterial community from all soil types were ranked as follows: spring 2012 (164.8 x 106 CFU g–1) > spring 2013 (147.7 x 106 CFU g–1) > autumn 2012 (80.6 x 106 CFU g–1) > autumn 2013 (79.4 x 106 CFU g–1). In case of land use and soil management practices (conventional, organic, and unmanaged) the bacterial abundance increased in the following order: vineyards < permanent grassland < arable land under crop rotation < hardwood forest < vegetable crop < hay crop. Our results suggest that seasonal variation, land use and soil management have a significant impact on bacterial richness and diversity (p < 0.05 in all cases). Extensive use of xenobiotic compounds in agriculture degrades soil microbial communities as they affect microbial abundance and composition, directly, and soil texture and fertility, indirectly.
... windows into this Bblack box.^These tools have widely been used to assess the composition and function of soil microbial populations and to monitor how different abiotic and biotic factors influence microbial community composition (Birkhofer et al. 2012;Fierer et al. 2007;Francioli et al. 2014;Hartmann et al. 2015;Nannipieri et al. 2003;Nicolardot et al. 2007;Rousk et al. 2010;Sørensen et al. 2009). ...
Soils harbor a huge diversity of microorganisms that participate in various biogeochemical cycles and influence soil fertility. Our knowledge of soil microbiota, however, is limited by the complexity and heterogeneity of soil habitats and the huge microbial diversity. In this study, fertilized and unfertilized soils from a long-term fertilization experiment were gamma-sterilized before self- or cross-inoculation with non-sterilized soil aliquots containing their respective microbial communities. Bacterial community dynamics resulting from each reinoculated treatment was monitored over 90 days using B-ARISA. This study design allowed us to assess the respective influences of two driving factors, original community and soil nutrient availability, on microbial community assemblage dynamics. For all treatments, the bacterial communities that evolved in the sterilized soils differed from those in the original soils and displayed dynamic shifts over time. These shifts were particularly illustrated by the appearance of numerous OTUs that were undetectable in the original soils and suggest that community assembly is primarily determined by niche factors. However, stronger community shifts and higher variations among the replicates were observed after reinoculation of nutrient-rich soil, suggesting an increased impact of stochastic processes on community assembly. Our results demonstrate that reinoculation-based approaches are not only valid for detecting a variety of low abundant soil bacteria but also for distinguishing the soil characteristics and ecological rules that shape soil microbial population assemblage.
