The impact of Gunnera tinctoria (Molina) Mirbel invasions on soil seed bank communities

Aims In recent years, there has been an increasing interest in the impact of invasive alien plant species on the soil seed bank. Soil seed banks play an important role in determining the composition and dynamics of the vegetation through time. Therefore, an ability to form a persistent seed bank and/or a capacity to alter the structure of the seed bank of invaded communities could be important factors in determining the success of many alien plant species. In this study, we report on a detailed assessment of the characteristics of the seed bank community associated with the herbaceous plant invader, Gunnera tinctoria, a newly emerging and potentially globally significant invasive plant species. This species, native to South America, is invasive in a range of wet habitats in Europe, Australasia and the USA.Methods A comprehensive assessment of the seed bank of invaded and comparable uninvaded areas was made at two points in time (May and October), at three sites in western Ireland. The seedling emergence approach was used to assess the structure (diversity, dominance and abundance) of the soil seed bank. Differences between invaded and uninvaded seed bank communities were investigated at the spatial scales of site, plot and depth.Important findings Gunnera tinctoria formed a large persistent seed bank at the study sites. Approximately 30-000 seedlings per square metre emerged from soils collected from invaded areas, of which 30% were found in deep soil layers. Seedlings of this invader represented 53–86% of the total number of seedlings associated with invaded areas. Both the transient and the more persistent component of the seed bank of invaded communities were significantly less diverse and abundant than those of uninvaded areas, and were characterized by higher dominance, even when seedlings of the invader were not included in the analysis. The seed bank of invaded areas was largely composed of seeds of agricultural weeds in addition to those of the invader. These results suggest that G. tinctoria has the capacity to profoundly alter the seed bank of invaded communities. These results have direct relevance for the development of control and management strategies, for this and other comparable invasive species, which should account for both quantitative and qualitative alterations in the seed bank community. Our study also suggests that control measures that result in disturbance of areas colonized by G. tinctoria could promote the germination of undesirable weeds.     

加拿大一枝黄花入侵对杭州湾地区土壤线虫群落的影响

近年来随着地下生态学的发展,生态学家们逐渐重视生物入侵导致的地下生物多样性及其相关生态系统功能的改变.为探究加拿大一枝黄花(Solidago canadensis)入侵对土壤线虫的影响,我们在杭州湾地区选取镇海、平湖、慈溪、奉贤、海盐和杭州6个研究地点,比较外来种加拿大一枝黄花群落与土著种芦苇(Phragmites a...     

Effect of 2,4,6-trinitrotoluene on soil bacterial communities

To gain insight into the impact of 2,4,6-trinitrotoluene (TNT) on soil microbial communities, we characterized the bacterial community of several TNT-contaminated soils from two sites with different histories of contamination and concentrations of TNT. The amount of extracted DNA, the total cell counts and the number of CFU were lower in the TNT-contaminated soils. Analysis of soil bacterial diversity by DGGE showed a predominance of Pseudomonadaceae and Xanthomonadaceae in the TNT-contaminated soils, as well as the presence of Caulobacteraceae. CFU from TNT-contaminated soils were identified as Pseudomonadaceae, and, to a lesser extent, Caulobacteraceae. Finally, a pristine soil was spiked with different concentrations of TNT and the soil microcosms were incubated for 4 months. The amount of extracted DNA decreased in the microcosms with a high TNT concentration [1.4 and 28.5 g TNT/kg (dry wt) of soil] over the incubation period. After 7 days of incubation of these soil microcosms, there was already a clear shift of their original flora towards a community dominated by Pseudomonadaceae, Xanthomonadaceae, Comamonadaceae and Caulobacteraceae. These results indicate that TNT affects soil bacterial diversity by selecting a narrow range of bacterial species that belong mostly to Pseudomonadaceae and Xanthomonadaceae.     

The effect of elevated atmospheric carbon dioxide levels on soil bacterial communities

The effect of elevated carbon dioxide levels on total bacterial communities was studied in a series of controlled and replicated model terrestrial ecosystems over a period of 38 weeks. The bacterial community was profiled using Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rRNA gene fragments amplified by the Polymerase Chain Reaction from DNA extracted directly from soil. Bacterial community DGGE profiles provided three major findings: (i) there was a high degree of profile similarity after ≈ 12 weeks (one plant generation); (ii) whilst overall DGGE profile was maintained over the 38 weeks (three plant generations), the banding patterns became more diverse with time; (iii) DGGE data provided no evidence for a shift in bacterial community structure resulting from exposure of the ecosystem to an increased atmospheric CO₂ level.     

The effect of nutrient deposition on bacterial communities in Arctic tundra soil

The microbial communities of high‐latitude ecosystems are expected to experience rapid changes over the next century due to climate warming and increased deposition of reactive nitrogen, changes that will likely affect microbial community structure and function. In moist acidic tundra (MAT) soils on the North Slope of the Brooks Range, Alaska, substantial losses of C and N were previously observed after long‐term nutrient additions. To analyse the role of microbial communities in these losses, we utilized 16S rRNA gene tag pyrosequencing coupled with community‐level physiological profiling to describe changes in MAT bacterial communities after short‐ and long‐term nutrient fertilization in four sets of paired control and fertilized MAT soil samples. Bacterial diversity was lower in long‐term fertilized plots. The Acidobacteria were one of the most abundant phyla in all soils and distinct differences were noted in the distributions of Acidobacteria subgroups between mineral and organic soil layers that were also affected by fertilization. In addition, Alpha‐ and Gammaproteobacteria were more abundant in long‐term fertilized samples compared with control soils. The dramatic increase in sequences within the Gammaproteobacteria identified as Dyella spp. (order Xanthomonadales) in the long‐term fertilized samples was confirmed by quantitative PCR (qPCR) in several samples. Long‐term fertilization was also correlated with shifts in the utilization of specific substrates by microbes present in the soils. The combined data indicate that long‐term fertilization resulted in a significant change in microbial community structure and function linked to changes in carbon and nitrogen availability and shifts in above‐ground plant communities.     

Impact of invasions by alien plants on soil seed bank communities: Emerging patterns

Much of our current understanding of the impact of invasive species on plant communities is based on patterns occurring in the above-ground vegetation, while only few studies have examined changes in soil seed banks associated with plant invasions, despite their important role as determinants of vegetation dynamics. Here, we reviewed the literature on the impact of plant invasions on the seed bank and we provide a quantitative synthesis using a meta-analysis approach. Specifically, (1) we quantified the impact of 18 invasive alien plants on (i) species richness and (ii) density of the seed banks of invaded communities, based on 58 pair-wise invaded-uninvaded comparisons (cases); we identified (2) the invasive taxa that are responsible for the largest changes in the seed bank; and (3) the habitats where substantial changes occur. Our study showed three major findings: (1) species richness (68% of cases) and density (58% of cases) were significantly lower in native seed banks invaded by alien plants; (2) species richness and density of native and alien species were remarkably lower in seed banks invaded by large, perennial herbs compared to uninvaded sites; and (3) invaded seed banks were often associated with a larger richness and/or abundance of alien species. This study indicates a need for additional seed bank data in invasion ecology to characterize species-specific and habitat-specific impacts of plant invasions, and to determine whether changes in the seed banks of native and alien species are a symptom of environmental degradation prior to a plant invasion or whether they are its direct result. The findings of this study help improve our capacity to predict the long-term implications of plant invasions, including limitations in the recruitment of native species from the seed bank and the potential for secondary invasions by seeds of other alien species.     

Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant–insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil ‘memories’ that influence aboveground plant community interactions in the next growing season. These soil-borne ‘memories’ can be altered by climate warming-induced plant range shifts and extreme drought.     

Weeds influence soil bacterial and fungal communities

Background and aims

Vineyards harbour a variety of weeds, which are usually controlled since they compete with grapevines for water and nutrients. However, weed plants may host groups of fungi and bacteria exerting important functions.

Methods

We grew three different common vineyard weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) in four different soils to investigate the effects of weeds and soil type on bacterial and fungal communities colonising bulk soil, rhizosphere and root compartments. Measurements were made using the cultivation-independent technique Automated Ribosomal Intergenic Spacer Analysis (ARISA).

Results

Weeds have a substantial effect on roots but less impact on the rhizosphere and bulk soil, while soil type affects all three compartments, in particular the bulk soil community. The fungal, but not the bacterial, bulk soil community structure was affected by the plants at the late experimental stage. Root communities contained a smaller number of Operational Taxonomic Units (OTUs) and different bacterial and fungal structures compared with rhizosphere and bulk soil communities.

Conclusions

Weed effect is localised to the rhizosphere and does not extend to bulk soil in the case of bacteria, although the structure of fungal communities in the bulk soil may be influenced by some weed plants.     

Short-term effects of amoxicillin on bacterial communities in manured soil

Antibiotic-resistant bacteria, nutrients and antibiotics that enter the soil by means of manure may enhance the proportion of bacteria displaying antibiotic resistance among soil bacteria and may affect bacterial community structure and function. To investigate the effect of manure and amoxicillin added to manure on soil bacterial communities, microcosm experiments were performed with two soil types and the following treatments: (1) nontreated, (2) manure-treated, (3) treated with manure supplemented with 10 mg amoxicillin kg(-1) soil and (4) treated with manure supplemented with 100 mg amoxicillin kg(-1) soil, with four replicates per treatment. Manure significantly increased the total CFU count and the amoxicillin-resistant CFU count of both soil types. However, only the soil with a history of manure treatment showed a significant increase in the relative number of amoxicillin-resistant bacteria as a result of amoxicillin amendment. The majority of plasmids exogenously isolated from soil originated from soil treated with amoxicillin-supplemented manure. All 16 characterized plasmids carried the bla-TEM gene, and 10 of them belonged to the IncN group. The bla-TEM gene was detected in DNA directly extracted from soil by dot-blot hybridization of PCR amplicons and showed an increased abundance in soil samples treated with manure. Molecular fingerprint analysis of 16S rRNA gene fragments amplified from soil DNA revealed significant effects of manure and amoxicillin on the bacterial community of both soils.     

Effects of selected root exudate components on soil bacterial communities

Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.     

Volatile-mediated antagonism of soil bacterial communities against fungi

Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.     

Resistance and recovery of soil microbial communities in the face of Alliaria petiolata invasions

Invaders can gain ecological advantages because of their evolutionary novelty, but little is known about how these novel advantages will change over time as the invader and invaded community evolve in response to each other. Invasive plants often gain such an advantage through alteration of soil microbial communities. In soil communities sampled from sites along a gradient of invasion history with Alliaria petiolata, microbial richness tended to decline, but the community's resistance to A. petiolata's effects generally increased with increasing history of invasion. However, sensitive microbial taxa appeared to recover in the two oldest sites, leading to an increase in richness, but consequent decrease in resistance. This may be because of evolutionary changes in the A. petiolata populations, which tend to reduce their investment to allelopathic compounds over time. These results show that, over time, microbial communities can develop resistance to an invasive plant but at the cost of lower richness. However, over longer time-scales evolution in the invasive species may allow for the recovery of soil microbial communities.     

The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil

In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. 'Total' and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation.     

土壤细菌网络互作调控线虫肠道细菌群落

动物肠道细菌群落在联系宿主与生态系统功能中发挥着至关重要的作用。【目的】本研究旨在评估绿肥翻压和水稻生长不同时期对土壤细菌和线虫肠道细菌群落组成和结构的影响,并探究土壤细菌和线虫肠道细菌群落间的潜在关联关系。【方法】基于盆栽试验,结合16S rRNA基因高通量测序技术,分析黑麦草翻压和对照处理下水稻生长的前期(返青期)和后期(收获期)土壤细菌和线虫肠道细菌群落,结合网络分析研究土壤细菌网络互作对线虫肠道细菌群落的潜在影响。【结果】黑麦草翻压对土壤细菌和线虫肠道细菌群落组成和结构没有显著影响(P>0.05);水稻生长后期样品比前期样品具有更高的α多样性。基于随机森林机器学习法获得的土壤细菌和线虫肠道细菌生物标志物之间存在广泛的显著相关关系,为土壤细菌群落变化调控线虫肠道细菌群落组成提供了有力的证据。共现网络分析表明土壤细菌之间的正相互作用显著促进了土壤细菌和线虫肠道细菌之间的正相互作用(P<0.01),进而影响了线虫肠道细菌之间的网络互作。结构方程模型进一步表明土壤养分含量的降低主要通过降低土壤细菌之间正相互作用,从而间接影响线虫肠道细菌之间的互作。【结论】土壤细菌互作可能在...     

Azoxystrobin and soil interactions: degradation and impact on soil bacterial and fungal communities

Aims: To provide an independent assessment of azoxystrobin effects on nontarget soil bacteria and fungi and generate some baseline information on azoxystrobin’s persistence in soil. Methods and Results: Plate based assay showed that azoxystrobin exhibited differential toxicity upon cultured fungi at different application rates. While ¹⁴C labelled isotopes experiments showed that less than 1% of azoxystrobin was mineralized, degradation studies revealed over 60% azoxystrobin breakdown over 21 days. PCR DGGE analysis of 16S and 18S rRNA genes from different soil microcosms showed that azoxystrobin had some effects on fungal community after 21 days (up to 84 days) of incubation in either light or dark soil microcosms. Light incubations increased fungal diversity while dark incubations reduced fungal diversity. Bacterial diversity was unaffected. Conclusions: Significant biotic breakdown of parent azoxystrobin occurred within 21 days even in the absence of light. Azoxystrobin under certain conditions can reduce fungal soil diversity. Significance and Impact of the Study: One of the few independent assessments of azoxystrobin (a widely used strobilurins fungicide) effects on soil fungi when used at the recommended rate. Azoxystrobin and metabolites may persist after 21 days and affect soil fungi.     

Impact of cultivation on characterisation of species composition of soil bacterial communities

The species composition of culturable bacteria in Scottish grassland soils was investigated using a combination of Biolog and 16S rDNA analysis for characterisation of isolates. The inclusion of a molecular approach allowed direct comparison of sequences from culturable bacteria with sequences obtained during analysis of DNA extracted directly from the same soil samples. Bacterial strains were isolated on Pseudomonas isolation agar (PIA), a selective medium, and on tryptone soya agar (TSA), a general laboratory medium. In total, 12 and 21 morphologically different bacterial cultures were isolated on PIA and TSA, respectively. Biolog and sequencing placed PIA isolates in the same taxonomic groups, the majority of cultures belonging to the Pseudomonas (sensu stricto) group. However, analysis of 16S rDNA sequences proved more efficient than Biolog for characterising TSA isolates due to limitations of the Microlog database for identifying environmental bacteria. In general, 16S rDNA sequences from TSA isolates showed high similarities to cultured species represented in sequence databases, although TSA-8 showed only 92.5% similarity to the nearest relative, Bacillus insolitus. In general, there was very little overlap between the culturable and uncultured bacterial communities, although two sequences, PIA-2 and TSA-13, showed >99% similarity to soil clones. A cloning step was included prior to sequence analysis of two isolates, TSA-5 and TSA-14, and analysis of several clones confirmed that these cultures comprised at least four and three sequence types, respectively. All isolate clones were most closely related to uncultured bacteria, with clone TSA-5.1 showing 99.8% similarity to a sequence amplified directly from the same soil sample. Interestingly, one clone, TSA-5.4, clustered within a novel group comprising only uncultured sequences. This group, which is associated with the novel, deep-branching Acidobacterium capsulatum lineage, also included clones isolated during direct analysis of the same soil and from a wide range of other sample types studied elsewhere. The study demonstrates the value of fine-scale molecular analysis for identification of laboratory isolates and indicates the culturability of approximately 1% of the total population but under a restricted range of media and cultivation conditions.     

Phenotypic diversity and antibiotic resistance in soil bacterial communities

The community structure in two different agricultural soils has been investigated. Phenotypic diversity was assessed by applying BIOLOG-profiles on a total of 208 bacterial isolates. Diversity indices were calculated from cluster analysis of the BIOLOG data. The bacterial isolates were also evaluated for resistance towards six different antibiotics, mercury resistance and the presence of plasmids. The presence of tetracycline-resistant determinants class A to E among Gram-negative bacteria was analysed with DNA probes. The distribution of tetracycline resistance markers among colonies growing on non-selective and tetracycline-selective plates were compared. The phenotypic approach demonstrated some difference in the diversity within the two soils. The frequency of antibiotic resistance isolates was high in both soils, whereas the frequency of mercury resistance differed significantly. We found no correlation between plasmid profiles and antibiotic resistance patterns. We found all the tetracycline resistance determinants except class B, indicating that the diversity of the tetracycline resistance determinants was complex in populations of resident soil bacteria under no apparent selective pressure for the genes in question.     

Exploration of soil bacterial communities for their potential as bioresource

Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.