Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition.

Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO3-) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.

Cover crops and carbon stocks: How under-vine management influences SOC inputs and turnover in two vineyards.

There is a growing awareness surrounding the importance of maintaining and increasing soil organic carbon (SOC, henceforth) stocks in vineyard systems. Increasing SOC positively influences numerous soil properties and has the added advantage of removing atmospheric CO2, thereby helping to mitigate the effects of climate change. Cover crops have long been used to influence soil properties in vineyard mid-rows, including increasing SOC content. Few studies, however, have quantified cover crop influence on SOC stocks and composition in the under-vine area, owing to a general reluctance to adopt under-vine cover crop management. This research aims to quantify SOC stocks and dissolved organic carbon (DOC) in soils from four treatments of under-vine management practice including two cover crop combinations, a straw mulch and herbicide-managed control across two vineyard sites established in 2014. We sampled soils under-vine to depths of 0-30 cm (stratified; 0-10 cm and 10-30 cm) and quantified both SOC concentrations and bulk density to ascertain SOC stocks. Further to this, we quantified water extractable organic carbon (WEOC) as a measure of the labile carbon stock, and measured heterotrophic respiration in a laboratory incubation as an indication of SOC turnover. We found that cover crop-managed soil under-vine sequesters up to 23% more soil organic carbon (SOC) as the traditional, herbicide practice over a five-year period of growth. Microbial activity increased by more than double in cover crop soils, owing to an increase in DOC and that there is evidence for more resistant C in cover crop soils. These results suggest that cover crop management under-vine is a viable solution to increase SOC stocks within vineyard systems. Taken together, the results of this study indicate that a shift from bare earth to cover crops in the under-vine region has the potential to sequester carbon in vineyard soils.

Spatiotemporal dynamics of soil health in urban agriculture.

There is a paucity of data on the state of urban agriculture soils. In order to develop efficient management practices, it is necessary to understand the seasonal dynamics of the soil health of these systems. This study sampled two community gardens, and one commercial urban agriculture site on a monthly basis over the span of one year. The dynamic analysis examined soil nutritional, chemical and microbial properties. Plant biodiversity was significantly higher in community gardens compared to commercial sites. Analysis of soil nutrients revealed fluctuations of mineral nitrogen with seasonal conditions and consistently high concentrations of plant-available phosphorus. We identified gradually decreasing soil total nitrogen and carbon concentrations throughout the year. Soils were abundant in arbuscular mycorrhizal fungi spores. Soil metabarcoding using 16S and ITS amplicons revealed a seasonal gradient of the microbial diversity and changes after the application of organic fertilizer. Soil-borne potential human pathogens were also detected in the soils. The results of this study provide relevant information about soil management principles in urban agriculture systems. These principles include mulching and the use of nutrient-balanced composts to counteract decreasing carbon pools and the excessive accumulation of phosphorus.

Evaluation of commercial composts and potting mixes and their ability to support arbuscular mycorrhizal fungi with maize (Zea mays) as host plant.

The use of composts and potting mixes in food production systems is a promising way to counteract the effects of soil degradation and allows crop growth in soilless culture systems. Arbuscular mycorrhizal fungi (AMF) are a well-studied group of beneficial plant symbionts that have been shown to provide important ecosystem services. This study analysed the properties of nine commercial Australian potting mixes and composts and investigated whether they support colonization of maize plants with AMF in a plant growth bioassay. Physicochemical analyses showed highly variable properties between the substrates, with some extreme values that limited plant growth. DNA-based analysis revealed the presence of various plant pathogens, which was linked to inhibited plant growth in one substrate. Some substrates did not meet national quality standards, due to the concentrations of plant nutrients, heavy metals, or substrate maturity. Plant growth was mostly limited due to nitrogen immobilization, which required weekly fertilizer applications. Solid state 13C nuclear magnetic resonance spectroscopy gave insight into the decomposition state of the substrates. Plant roots in most substrates were well colonized with AMF (>60% root length), regardless of most substrate properties. Root colonization was negatively affected in only one substrate, likely due to ammonium toxicity. Results of this study show that not all commercial substrates adhered to national quality standards. Potting mixes and composts can support high mycorrhizal root colonization when plant growth is otherwise not limited.

Urban soil health: A city-wide survey of chemical and biological properties of urban agriculture soils.

The integration of urban green spaces into modern city planning is seen as a promising tool to offset the drawbacks of ever-expanding cities. Urban agriculture is a common method to implement such strategies and to increase urban sustainability with a special focus on food security. Due to their location, urban farms are highly influenced by past and present anthropogenic activities which can threaten both soil health and food safety. This study includes 12 urban agriculture sites in the metropolitan area of Adelaide, Australia. It is the first of its kind to focus on soil health in urban agriculture systems with a further emphasis on mycorrhizal fungi. Descriptive information about each site, the biodiversity of the selected plots and soil samples from different depths and locations were collected and analysed for chemical and biological parameters. Seven metals, total and plant-available (Colwell) phosphorus and available nitrogen were measured in soils. A glasshouse bioassay was also conducted to determine the abundance of beneficial arbuscular mycorrhizal fungi in the soils and the change of root colonization after inoculation with the mycorrhizal fungus Rhizophagus irregularis. Results showed a generally high biodiversity of plants that correlated with site activity (commercial or community garden) and which could potentially be used for urban biodiversity conservation. Metal concentrations in soils were below national guidelines levels for all samples, although sites with previous industrial history showed elevated levels when compared to sites without industrial history. The use of raised beds with introduced soils eliminated differences in previous land-use history, thereby providing a good option to support cleaner production. Gardening soils were considered highly fertile, with plant-available (Colwell) P concentrations exceeding recommended levels for most horticultural crops, while soils were adequately supplied with nitrogen. Most plant nutrients were derived from freely available urban waste streams and integrated via composting. Various urban waste streams could be used to counter-act imbalanced soil nutrients. Arbuscular mycorrhizal fungi were present in all sites, indicating that the practiced soil management is sustainable from a microbial perspective. Given their important role in supporting plant nutrition, and potential to reduce the need for external nutrient inputs, they provide an important focal point for achieving clean and sustainable urban food production. The results were incorporated into a framework for the management of urban soil health.

The effect of fire affected Pinus radiata litter and char addition on soil nitrogen cycling.

In pine forest litters, decomposition rate is directly affected by the pathway the needle followed to the ground, whether that was via programmed apoptosis and abscission or via stress induced loss through branch damage or tree death. Stress induced losses may occur due to fire damage, which leads to a post-fire litter layer composed of non-senescent debris that fell during or after the event. This study investigates decomposition and nitrogen cycling in soils amended with two litters from Pinus radiata plantations that had different recent fire histories. Litters were incubated in the presence or absence of field collected char for up to 94 days. These soil treatments were analysed for microbial activity (soil respiration) and N pools (microbial, mineral, and potentially mineralisable). Soil and litter treatments were additionally incubated in the presence of ammonium nitrate solution to determine N absorption potential of the litters. Respiration was greatest in soils that received fire affected (FA) litter regardless of the presence or absence of char. Nitrogen pools were largely similar between the control (no litter) treatment and not fire affected (NFA) litter treatments. Measured N pools were exceedingly low (92% of samples <2 µg-N g soil-1 where detected) or not detectable (37% of samples below detection limits) in all FA litter treatments at most times. Char appeared inert throughout and had no effects on microbial activity or nitrogen cycling. This study indicates that fire affected pine litter collected four months post fire has strong N absorption properties with or without the presence of char. The presence of fire affected litter is likely to affect N availability for regeneration of forest growth.

Using High-Throughput Phenotyping to Explore Growth Responses to Mycorrhizal Fungi and Zinc in Three Plant Species.

There are many reported benefits to plants of arbuscular mycorrhizal fungi (AMF), including positive plant biomass responses; however, AMF can also induce biomass depressions in plants, and this response receives little attention in the literature. High-throughput phenotyping (HTP) technology permits repeated measures of an individual plant's aboveground biomass. We examined the effect on AMF inoculation on the shoot biomass of three contrasting plant species: a vegetable crop (tomato), a cereal crop (barley), and a pasture legume (Medicago). We also considered the interaction of mycorrhizal growth responses with plant-available soil zinc (Zn) and phosphorus (P) concentrations. The appearance of a depression in shoot biomass due to inoculation with AMF occurred at different times for each plant species; depressions appeared earliest in tomato, then Medicago, and then barley. The usually positive-responding Medicago plants were not responsive at the high level of soil available P used. Mycorrhizal growth responsiveness in all three species was also highly interactive with soil Zn supply; tomato growth responded negatively to AMF inoculation in all soil Zn treatments except the toxic soil Zn treatment, where it responded positively. Our results illustrate how context-dependent mycorrhizal growth responses are and the value of HTP approaches to exploring the complexity of mycorrhizal responses.

Interactive effects of compost and pre-planting soil moisture on plant biomass, nutrition and formation of mycorrhizas: a context dependent response.

We aimed to investigate the combined impacts of compost addition and pre-planting soil moisture conditions, on plant-available nutrients, and subsequent impacts on the biomass, nutrition and formation of AM by two important crop species. A glasshouse study was undertaken in which wheat and tomato plants were grown in compost amended or un-amended soil that was subjected to different moisture regimes prior to planting. The availability of P was strongly influenced by compost addition, but not pre-planting moisture conditions. In contrast, mineral N pools were affected by compost addition and pre-planting soil moisture conditions in complex ways. These changes in nutrient availability affected plant biomass, nutrient uptake and formation of AM. In general, plant performance was better where pre-planting soil moisture conditions were wet or dry, and worse where they involved a wet/dry cycle, and mycorrhizal colonisation was lower where compost was added to the soil. That pre-planting moisture conditions affect the biomass of subsequent crops is an important finding, the potential implications of which are considered here.

Riparian reforestation: are there changes in soil carbon and soil microbial communities?

Reforestation of pastures in riparian zones has the potential to decrease nutrient runoff into waterways, provide both terrestrial and aquatic habitat, and help mitigate climate change by sequestering carbon (C). Soil microbes can play an important role in the soil C cycle, but are rarely investigated in studies on C sequestration. We surveyed a chronosequence (0-23years) of mixed-species plantings in riparian zones to investigate belowground (chemical and biological) responses to reforestation. For each planting, an adjacent pasture was surveyed to account for differences in soil type and land-use history among plantings. Two remnant woodlands were included in the survey as indicators of future potential of plantings. Both remnant woodlands had significantly higher soil organic C (SOC) content compared with their adjacent pastures. However, there was no clear trend in SOC content among plantings with time since reforestation. The substantial variability in SOC sequestration among plantings was possibly driven by differences in soil moisture among plantings and the inherent variability of SOC content among reference pastures adjacent to plantings. Soil microbial phospholipid fatty acids (PLFA, an indicator of microbial biomass) and activities of decomposition enzymes (ß-glucosidase and polyphenol oxidase) did not show a clear trend with increasing planting age. Despite this, there were positive correlations between total SOC concentration and microbial indicators (total PLFA, fungal PLFA, bacterial PLFA and activities of decomposition enzymes) across all sites. The soil microbial community compositions (explored using PLFA markers) of older plantings were similar to those of remnant woodlands. There was a positive correlation between the soil carbon:nitrogen (C:N) and fungal:bacterial (F:B) ratios. These data indicate that in order to maximise SOC sequestration, we need to take into account not only C inputs, but the microbial processes that regulate SOC cycling as well.

Biochar application during reforestation alters species present and soil chemistry.

Reforestation of landscapes is being used as a method for tackling climate change through carbon sequestration and land restoration, as well as increasing biodiversity and improving the provision of ecosystem services. The success of reforestation activities can be reduced by adverse field conditions, including those that reduce germination and survival of plants. One method for improving success is biochar addition to soil, which is not only known to improve soil carbon sequestration, but is also known to improve growth, health, germination and survival of plants. In this study, biochar was applied to soil at rates of 0, 1, 3 and 6 t ha(-1) along with a direct-seed forest species mix at three sites in western Victoria, Australia. Changes in soil chemistry, including total carbon, and germination and survival of species were measured over an 18 month period. Biochar was found to significantly increase total carbon by up to 15.6% on soils low in carbon, as well as alter electrical conductivity, Colwell phosphorous and nitrate- and ammonium-nitrogen. Biochar also increased the number of species present, and stem counts of Eucalyptus species whilst decreasing stem counts of Acacia species. Biochar has the potential to positively benefit reforestation activities, but site specific and plant-soil-biochar responses require targeted research.

Physicochemical and microbiological effects of long- and short-term winery wastewater application to soils.

Application of winery wastewaters to soils for irrigation of various crops or landscapes is a common practice in the wine industry. In this study, we sought to investigate the effects of this practice, by comparing the physicochemical and microbiological soil properties in paired sites that differed in having had a history of winery waste application or not. We also compared the effects of a single application of untreated winery wastewater, to application of treated winery wastewater (sequencing batch reactor) and pure water to eliminate the effects of wetting alone. Long-term application of winery wastes was found to have significant impacts on soil microbial community structure, as determined by phospholipid fatty acid analysis, as well as on many physicochemical properties including pH, EC, and cation concentrations. (13)C NMR revealed only slight differences in the nature of the carbon present at each of the paired sites. A single application of untreated winery wastewater was shown to have significant impacts upon soil respiration, nitrogen cycling and microbial community structure, but the treated wastewater application showed no significant differences to wetting alone. Results are discussed in the context of sustainable winery wastewater disposal.

Plant nutrient acquisition and utilisation in a high carbon dioxide world.

Producing enough food to meet the needs of an increasing global population is one of the greatest challenges we currently face. The issue of food security is further complicated by impacts of elevated CO2 and climate change. In this viewpoint article, we begin to explore the impacts of elevated CO2 on two specific aspects of plant nutrition and resource allocation that have traditionally been considered separately. First, we focus on arbuscular mycorrhizas, which play a major role in plant nutrient acquisition. We then turn our attention to the allocation of resources (specifically N and C) in planta, with an emphasis on the secondary metabolites involved in plant defence against herbivores. In doing so, we seek to encourage a more integrated approach to investigation of all aspects of plant responses to eCO2.

Effects of arbuscular mycorrhizas on ammonia oxidizing bacteria in an organic farm soil.

Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil.

Inoculum type does not affect overall resistance of an arbuscular mycorrhiza-defective tomato mutant to colonisation but inoculation does change competitive interactions with wild-type tomato.

• The influence of inoculum type on colonisation of a mycorrhiza-defective tomato mutant, rmc, by the AM fungus Glomus coronatum was studied by comparing inoculum composed predominantly of spores with hyphae growing from mycorrhizal 'nurse plants', including the wild-type tomato progenitor (WT), other Lycopersicon species, and leek. • Colonisation of rmc was not primarily influenced by inoculum source; minor differences could be attributed to differences in inoculum potential. The mutation is therefore different from other mycorrhiza-defective tomato mutants. • Growth of rmc was reduced in the presence of nurse plants, because of competition with them, so a second experiment examined the effects of AM colonisation on competition between rmc and the WT tomato. This experiment was a replacement series in which rmc and WT were grown in competition and as single plants, inoculated with G. coronatum or uninoculated. • The WT did not respond to G. coronatum when grown alone, but responded positively when in competition with rmc. We conclude from the second experiment that mycorrhizal responsiveness is influenced by competition with (in this case) a surrogate nonhost plant rmc in a situation that mimics interspecific competition. It is therefore a community-based parameter. Results are discussed in the context of responses of mycorrhizal vs nonmycorrhizal species and competition in natural plant ecosytems.

Growth and phosphorus nutrition of a Paris-type arbuscular mycorrhizal symbiosis.

• Paris -type arbuscular mycorrhizas (AM) are reportedly the most common morphological type of AM; however, most research has focused on the Arum -type. Asphodelus fistulosus , a common weed in southern Australia, forms Paris -type AM when colonised by Glomus coronatum . It is often found in sites with low nutrient levels, and may therefore be dependent on its AM associations for growth and phosphorus (P) nutrition. • A. fistulosus was inoculated with G. coronatum and grown in pots containing a soil/sand mixture with P added to give five soil P concentrations. The plants were grown in a glasshouse and harvested 6 and 9 wk after planting, at which times growth, P nutrition and colonisation were measured. • At low soil P, A. fistulosus showed very marked positive responses to colonisation both in P uptake and growth; both responses decreased with increasing P supply. Colonisation was not greatly reduced by increasing P supply. • This study appears to be one of the first detailed investigations of P responses in a Paris -type AM, providing insight into what is reportedly the more common but less well studied morphological type of AM.

Quantitative development of Paris-type arbuscular mycorrhizas formed between Asphodelus fistulosus and Glomus coronatum.

• Arum- and Paris-type symbioses are the two main morphological types of arbuscular mycorrhiza. Here, the developmental time-course of the Paris-type association formed from colonization of Asphodelus fistulosus (onion weed) by Glomus coronatum is presented. • Development was monitored over 27 d. Root colonization was assessed using a modification of the magnified intersects technique (MIT), for investigating the interdependence (thus IMIT) of structures. • Hyphal and arbusculate coils were found predominantly in the outer and inner cortex of the root, respectively. The interdependence of external hyphae, hyphal coils and arbusculate coils was determined during the relatively slow development of the symbiosis. • The time required for development of Paris-type arbuscular mycorrhizas is slower than for the Arum type, and both time and space influence the formation of hyphal coils. Use of IMIT for scoring colonization allows determination of the interdependence of different fungal structures, and thus the technique has potentially wide applications, such as in relating the presence of different structures to signals from molecular probes.