N-fixing trees in restoration plantings: effects on nitrogen supply and soil microbial communities

Mixed-species restoration tree plantings are being established increasingly, contributing to mitigate climate change and restore ecosystems. Including nitrogen (N)-fixing tree species may increase carbon (C) sequestration in mixed-species plantings, as these species may substantially increase soil C beneath them. We need to better understand the role of N-fixers in mixed-species plantings to potentially maximize soil C sequestration in these systems. Here, we present a field-based study that asked two specific questions related to the inclusion of N-fixing trees in a mixed-species planting: 1) Do non-N-fixing trees have access to N derived from fixation of atmospheric N2 by neighbouring N-fixing trees? 2) Do soil microbial communities differ under N-fixing trees and non-N-fixing trees in a mixed-species restoration planting? We sampled leaves from the crowns, and litter and soils beneath the crowns of two N-fixing and two non-N-fixing tree species that dominated the planting. Using the 15N natural abundance method, we found indications that fixed atmospheric N was utilized by the non-N-fixing trees, most likely through tight root connections or organic forms of N from the litter layer, rather than through the decomposition of N-fixers litter. While the two N-fixing tree species that were studied appeared to fix atmospheric N, they were substantially different in terms of C and N addition to the soil, as well as microbial community composition beneath them. This shows that the effect of N-fixing tree species on soil carbon sequestration is species-specific, cannot be generalized and requires planting trails to determine if there will be benefits to carbon sequestration. © 2014 Elsevier Ltd.

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 (β-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.

Pastures to woodlands: changes in soil microbial communities and carbon following reforestation

Reforestation of agricultural lands has the potential to sequester C, while providing other environmental benefits. It is well established that reforestation can have a profound impact on soil physicochemical properties but the associated changes to soil microbial communities are poorly understood. Therefore, the objective of this study was to quantify changes in soil physicochemical properties and microbial communities in soils collected from reforested pastures and compare then to remnant vegetation and un-reforested pastures. To address this aim, we collected soil from two locations (pasture and its adjacent reforested zone, or pasture and its adjacent remnant vegetation) on each of ten separate farms that covered the range of planting ages (0-30 years and remnant vegetation) in a temperate region of southeastern Australia. Soils were analysed for a range of physicochemical properties (including C and nutrients), and microbial biomass and community composition (PLFA profiles). Soil C:N ratios increased with age of tree planting, and soil C concentration was highest in the remnant woodlands. Reforestation had no clear impact on soil microbial biomass or fungal:bacterial ratios (based on PLFA's). Reforestation was associated with significant changes in the molecular composition of the soil microbial community at many farms but similar changes were found within a pasture. These results indicate that reforestation of pastures can result in changes in soil properties within a few decades, but that soil microbial community composition can vary as much spatially within pastures as it does after reforestation.

Photodegradation, interaction with iron oxides and bioavailability of dissolved organic matter from forested floodplain sources

Photochemical degradation of dissolved organic matter (DOM) can influence food webs by altering the availability of carbon to microbial communities, and may be particularly important following periods of high DOM input (e.g. flooding of forested floodplains). Iron oxides can facilitate these reactions, but their influence on subsequent organic products is poorly understood. Degradation experiments with billabong (= oxbow lake) water and river red gum (Eucalyptus camaldulensis) leaf leachate were conducted to assess the importance of these reactions in floodplain systems. Photochemical degradation of DOM in sunlight-irradiated quartz tubes (with and without amorphous iron oxide) was studied using gas chromatography and UV-visible spectroscopy. Photochemical reactions generated gaseous products and small organic acids. Bioavailability of billabong DOM increased following irradiation, whereas that of leaf leachate was not significantly altered. Fluorescence excitation-emission spectra suggested that the humic component of billabong organic matter was particularly susceptible to degradation, and the source of DOM influenced the changes observed. The addition of amorphous iron oxide increased rates of photochemical degradation of leachate and billabong DOM. The importance of photochemical reactions to aquatic systems will depend on the source of the DOM and its starting bioavailability, whereas inputs of freshly formed iron oxides will accelerate the processes.

Identification and characterization of genes conferring salt tolerance to Escherichia coli from pond water metagenome

Metagenomics provides culture-independent access to gene pool of the whole microbial communities. To identify genes responsible for salt tolerance in unculturable bacteria, Escherichia coli clones were enriched with an ability to grow at inhibitory NaCl concentrations (750 mM) from a pond water metagenomic library. From two unique clones, genes encoding for proteins with similarity to a putative general stress protein (GspM) harbouring GsiB domain and a putative enoyl-CoA hydratase (EchM) were identified to be responsible for salt tolerance. The gspM was expressed by its native promoter whereas the echM was expressed from the lacZ promoter of the plasmid. EchM was overexpressed with a hexahistidyl tag. Purified EchM showed crotonyl-CoA hydratase activity. These genes have potential application in generating salt tolerant recombinant bacteria or transgenic plants.

High colonization by native arbuscular mycorrhizal fungi (AMF) of rubber trees in small-holder plantations on low fertility soils in North East Thailand

Rubber tree is a very important crop in Thailand, representing an essential source of income for farmers. In the past two decades, rubber tree plantations have been greatly expanding in unfavorable areas, where climate conditions are difficult and soil fertility is very poor. To optimize latex yields, mineral fertilizers have been widely used. A better understanding of the roles of the biological compartment in soil fertility is essential to determine alternative management practices to sustain soil fertility and optimize latex yields. Arbuscular mycorrhizal fungi (AMF) are widely recognized as beneficial for plants, mainly through their role in improving plant nutrient uptake. The objective of this study was to assess the AMF populations in rubber tree plantations and the impact of both soil characteristics and plantation age on these communities. Our results showed that all rubber trees were highly colonized, regardless of the soil structure and nutrient contents. AMF colonization was not affected by the age of the trees, suggesting that maintaining the symbiosis is likely to be beneficial at all stages. A better understanding and management of the microbial communities would contribute to maintaining or restoring soil fertility, leading to a better tree growth and optimized latex yield.

Immune-microbiota interactions: dysbiosis as a global health issue

Throughout evolution, microbial genes and metabolites have become integral to virtually all aspects of host physiology, metabolism and even behaviour. New technologies are revealing sophisticated ways in which microbial communities interface with the immune system, and how modern environmental changes may be contributing to the rapid rise of inflammatory noncommunicable diseases (NCDs) through declining biodiversity. The implications of the microbiome extend to virtually every branch of medicine, biopsychosocial and environmental sciences. Similarly, the impact of changes at the immune-microbiota interface are directly relevant to broader discussions concerning rapid urbanization, antibiotics, agricultural practices, environmental pollutants, highly processed foods/beverages and socioeconomic disparities--all implicated in the NCD pandemic. Here, we make the argument that dysbiosis (life in distress) is ongoing at a micro- and macro-scale and that as a central conduit of health and disease, the immune system and its interface with microbiota is a critical target in overcoming the health challenges of the twenty-first century.

Isolation and phylogenetic identification of halotolerant/halophilic bacteria from the salt mines of Karak, Pakistan

Extreme environments like salt mines are inhabited by a variety of bacteria that are well-adapted to such environments. The bacterial populations provide economic benefits in terms of enzymes synthesis. The salt mines of Karak region in Pakistan are extremely saline and the microbial communities found here have not yet been explored. In the present study, 57 halotolerant/halophilic bacterial strains were isolated from the salt mines of Karak. These strains were grown in media with 0-35% NaCl concentration. The morphological and physiological characteristics of the isolated strains were studied to optimize the growth conditions and to classify the isolated bacterial strains into slightly halotolerant/halophilic, moderately halophilic and extreme halophilic. The phylogenetic analyses inferred from 16S rRNA gene sequence of the isolated strains demonstrated that the major population were closely related to species belonging to Planococcus, Jeotgalicoccus, Staphylococcus, Halobacillus, Halomonas, Brevibacterium, Gracilibacillus, Kocuria, Salinivibrio, Salinicoccus, Oceanobacillus and Bacillus genera. Results showed that the salt mines of Karak region are rich in halotolerant/halophilic bacterial population with diverse bacterial communities, which may be utilized in various industrial applications after proper screening and identification.