Soil carbon loss under pasture and pine: Responses to urine addition

There have been reports of losses of soil carbon (C) in New Zealand pastures under dairy grazing. Acceleration of mineralisation or leaching of soil C following urine deposition may decrease soil C. However, little research of the effect of cow urine on soil C has been conducted. The overall objective of this thesis was to investigate the potential for dairy cow urine to solubilise soil C, which can then be lost through mineralisation or leaching. Soils from both grazed pasture and Pinus radiata plantations (termed pasture and pine soils) were investigated. The concentration, composition, and bioavailability of urine-C were investigated. Cow urine contained 7.5±1.2 g C L–¹, with a C:N ratio of 2:1. About 45% of the C content of cow urine was attributed to hippuric acid, the other major contributors were urea, an unidentified amide and phenaceturic acid. On incubation at 25°C, up to 25% of urine-C was degraded in 28 days, demonstrating that cow urine is biodegradable and could potentially act to prime C mineralisation in soils. Solubilisation of soil C (0-20 cm soil depth) following urine application was tested by measuring adsorption of urine-C and subsequent desorption of soil C in air-dried pine and pasture soils. While adsorption was low at 3% of urine-C, the solubilisation of soil C by urine ranged between 11-28% of soil C concentration for 5 different soils, however, solubilisation was likely overestimated due to the use of air-dried soils. Soil C solubilisation was also measured in field moist soils applied with artificial urine, and was less than that reported from air-dried soils. Priming of soil C mineralisation, solubilisation, and extracellular enzyme activity were measured using moist repacked pine and pasture soil cores (0-5 cm soil depth) treated with cow urine or radio-labelled artificial urine. Positive priming of soil C mineralisation, where more carbon dioxide (CO₂) was produced than C added, was measured following application of cow urine in both pine and pasture soils. The pasture soils lost 5.1±0.9%, and the pine soils 4.0±0.1%, of soil C concentration as CO₂ during a 84 day incubation. Positive priming was attributed to increased microbial and urease activity and accelerated soil C mineralisation in urine treated soils. The remaining extracellular enzyme activities assayed were unlikely to have contributed to soil C priming. In contrast to the positive priming measured following cow urine application, treatment of soil with artificial urine resulted in less CO₂ produced than C added – or negative priming. Increased soil pH following urine application may have played an important role in increasing C mineralisation as water soluble C increased with increasing soil pH. Therefore, cow urine can cause priming of soil C mineralisation and lead to a loss of soil C. However, artificial urine may not adequately model cow urine with respect to C cycling. Soil C solubilisation by urine and subsequent leaching from undisturbed pasture soil (0-5 cm soil depth) was assessed by applying δ¹³C enriched urine. Leaching resulted in a loss of 0.45±0.03% of soil C concentration, which was 10 times greater than the loss of soil C in the water control treatment (0.048±0.001%). The leaching of soil C was small compared to the 5% loss of soil C by priming in the repacked core experiment. Soil solubilisation in the undisturbed cores was less than both repacked cores and air-dried soils, demonstrating that soil C solubilisation increases with increasing soil disturbance. The acid neutralising capacity (ANC) forcing potential of cow urine was 11.8 meq L–¹, which was more than 20 times greater than sodium nitrate fertiliser application (30 kg N ha-¹ year-¹), although the nitrogen loading rates of the urine were higher than the fertiliser . ANC forcing has been linked to increasing soil pH and dissolved organic C leaching, and may have been a factor in soil C solubilisation under urine patches. Upon assessing water stable aggregates after urine application, disaggregation of soil was not a major factor in soil C solubilisation. The key conclusions were that: • there was strong evidence to support the hypothesis that urine deposition led to soil C solubilisation and priming of soil C mineralisation, that could have contributed to the reported declines in soil C in dairy pastures; • priming of soil C decomposition was 10 times greater than leaching and may be the predominant mechanism of soil C loss following urine deposition; and • urine deposition resulted in greater losses of soil C from pasture soils than pine soils, in contrast to expectations that soil C in pasture soils would have been acclimatised to urine application. The work in this thesis was laboratory based and requires further testing under field conditions. Further work is also needed to establish the mechanisms of soil C solubilisation and the role of solubilised soil C in priming of soil C mineralisation

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

BACKGROUND: Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. METHODOLOGY/PRINCIPAL FINDINGS: The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. CONCLUSIONS/SIGNIFICANCE: The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ?75% of the genus-level bacterial and archaeal taxa present in the rumen.publishersversionPeer reviewe

Reverse genetic analyses of TERMINAL EAR-like RNA-binding protein genes in Arabidopsis thaliana (L.) Heynh. : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Molecular Genetics at Massey University, Palmerston North, New Zealand

In maize, a loss-of-function mutation in a MEI2-like gene, terminal ear1 (te1), leads to morphological defects able to be traced back to the shoot apical meristem. One MEI2-like gene has been identified in maize, while six have been identified in rice and nine in Arabidopsis thaliana. In this thesis, a programme of reverse genetic analysis has been designed to investigate if Arabidopsis genes most closely aligned in parsimony trees with TE1, TERMINAL EAR-LIKE 1 (TEL1), TERMINAL EAR-LIKE 2 (TEL2), perform the same function as TE1. The expression pattern of TEL1 and TEL2 genes is restricted to the Shoot Apical Meristem (SAM) and the Root Apical Meristem (RAM) suggesting these genes are important in meristem maintenance or function. Results of the molecular genetic analysis of TEL genes in Arabidopsis support models in which these genes help maintain cells in a pluripotent state. For the first part of the thesis, analysis of lines carrying single knockouts of TEL1 and TEL2 and double knockout lines reveals a slightly accelerated rate of organogenesis, consistent with these genes normally acting to inhibit terminal differentiation pathways. Plants grown on medium containing gibberellic acid and sucrose, at higher than normal concentrations, present a further accelerated rate of organogenesis. As the second part of the thesis, in situ and promoter/reporter GUS fusion analyses indicate TEL1 is preferentially expressed in both the root and shoot apical meristems. Deletion analysis using GFP reporter constructs show that 5' sequences are sufficient to drive quiescent centre (QC) expression in the root while additional sequences are required for central zone (CZ) expression in the SAM. Physiological studies indicate expression of TEL1 in the root is sensitive to the hormones, auxin, gibberellic acid and zeatin, when added at physiological concentrations. To confirm the auxin effect, GFP expression is no longer visible after 12 hours of exposure to auxin transport inhibitors in plants containing GFP under the control of the TEL1 promoter, suggesting, in common with other QC markers, that TEL expression is sensitive to auxin levels. Analysis of mutant plants with altered root patterning suggests QC specific expression of TEL1 requires early acting genes, such as PLETHORA 1 and 2, but does not depend on later acting genes such as SCARECROW or SHORTROOT

Pulp and paper effluent organic constituents interactions with soil matrices

The land application of pulp and paper effluents has the potential to be a long-term sustainable solution for the requirements of industry and regulatory control of environmental impacts. A critical aspect of its success will be that the soil matrix onto which the effluents are applied is able to assimilate and remove effluent organic constituents of environmental concern. Two important processes are required for this. Firstly, the soils need to rapidly attenuate the movement of these materials through the soil column to ensure that groundwater and surface water contamination is minimised. Secondly, the accumulated constituents need to be mineralised/degraded to ensure the capacity of the soil is not exceeded with repeated effluent applications. This study aimed to use laboratory-scale systems to determine the contribution of these mechanisms to the fate and behaviour of environmentally-significant pulp and paper effluent constituents. Resin acids (major effluent toxicants, bioaccumulative and persistent) and phytosterols (potential endocrine disruptors) were the focus of this work. Three potential land application soil types, sand, Kawerau soil, and Whakarewarewa soil were considered. Thermomechanical pulping effluent was the principal waste source for the study since it is most suitable for land application. Given the potential for effluents from other pulp and paper processes to be land applied to some degree, two other wastestreams, chemi-thermomechanical and bleached kraft effluents, were considered in a more limited fashion. Resin acids were readily degradable in all the selected soils and with all effluent types. In most cases nearly 100% removal was obtained within 6 months incubation. The sand substrate was particularly effective in removing the compounds, possibly because of a lack of alternative carbon sources in the sand matrix. Effluent-derived acclimated microbiota may have been the principal degraders responsible for resin acid degradation. Resin acids were substantially degraded under both aerobic and anaerobic conditions. Thus, land application systems may be able to sustain resin acid removal performance even if anaerobic conditions are produced in the soils as a result of high rainfall/water table increases or over-irrigation. Resin acids were rapidly absorbed to the soil matrices. A significant proportion of the resin acids were irreversibly adsorbed to the organic soils. The capacity and intensity of adsorption was correlated with soil carbon content. Whakarewarewa soil had the greatest sorption capacity and sand was least attentuative. High concentrations of dissolved organic carbon were leached from the Kawerau and Whakarewarewa soils. This soluble material may influence the partitioning behaviour of lipophilic compounds, such as resin acids, and thus their mobility. Overall, this study has shown that resin acids can be very effectively removed from pulp and paper effluents when applied to a range of soils. Phytosterols were not attenuated as efficiently but are likely to be relatively immobile in the upper layers of the soil column. Other factors, such as salinity and nutrient loadings, are therefore likely to be more important limitations for the future utilisation of land application systems in the pulp and paper industry

Biomass and root attributes of eight of New Zealand’s most common indigenous evergreen conifer and broadleaved forest species during the first 5 years of establishment

Abstract Background Tree allometric equations are critical tools for determining tree volume, biomass and carbon stocks. However, there is a lack of species-specific biomass equations for juvenile trees of many of New Zealand’s indigenous species. The aim of this study was to provide allometric equations for total above- and below-ground biomass and total root biomass and length for eight common evergreen conifer and broadleaved species. Methods In a plot-based field trial, growth metrics of conifers Prumnopitys taxifolia (matai), Agathis australis (kauri), Prumnopitys ferruginea (miro), Podocarpus totara (totara), Dacrycarpus dacrydioides (kahikatea) and Dacrydium cupressinum (rimu) and broadleaved species Alectryon excelsus (titoki) and Vitex lucens (puriri) were measured annually. These species were selected based on their potential role as a long-term solution for mitigating erosion in areas of marginal land proposed for new afforestation/reforestation and as an important carbon (C) sink. Results Root collar diameter (RCD) provided the best fit for tree height, total above-ground biomass (AGB) and total below-ground biomass (BGB), and all regressions were highly significant (P = 0.001). Most species showed significant increases in annual growth and, by year 5, the BGB ranged between 21 and 42% of total biomass and decreased with increasing plant age. Of the conifers, Podocarpus totara had the greatest mean maximum root spread (2.2 m) exceeded only by the broadleaved Vitex lucens (2.5 m). For all species, and in each year of the trial, 100% of the BGB remained confined to within 0.5 m of the ground surface. With the exception of Vitex lucens and Podocarpus totara, > 90% of the total root length remained within a 0.5-m radius of the root bole. The species-specific mean tree biomass of 5-year-old plants ranged from 0.32 to 4.28 kg plant−1. A mixed-species forest established at 1000 stems per hectare (spha), consisting of 200 of each of the best performed of the trialled species, would amass ~ 2.3 t ha−1 of biomass and a forest carbon stock of 3.8 t CO2 ha−1 within 5 years. Conclusions Inter-species differences in the allocation of BGB and AGB appeared to be age dependent. The root-growth metrics of these common indigenous forest species, as candidates for erosion control, have improved our understanding of their potential usefulness for stabilising marginal land. Whole-plant biomass of juvenile trees will greatly improve the accuracy of current estimates of forest carbon stocks for proposed new areas of indigenous afforestation/reforestation

Additional file 5: of Biomass and root attributes of eight of New Zealand’s most common indigenous evergreen conifer and broadleaved forest species during the first 5 years of establishment

Mean root and root bole biomass (g), as a percent of total below-ground biomass (BGB). (DOCX 19 kb

Additional file 1: of Biomass and root attributes of eight of New Zealand’s most common indigenous evergreen conifer and broadleaved forest species during the first 5 years of establishment

Ecological and site requirements of the trialled species. (DOCX 16 kb

Additional file 4: of Biomass and root attributes of eight of New Zealand’s most common indigenous evergreen conifer and broadleaved forest species during the first 5 years of establishment

Mean below-ground attributes of six indigenous conifer and two broadleaved species. (DOCX 17 kb