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Item Biodiversity in mountain soils above the treeline(John Wiley and Sons Ltd on behalf of Cambridge Philosophical Society, 2025-05-14) Praeg N; Steinwandter M; Urbach D; Snethlage MA; Alves RP; Apple ME; Bilovitz P; Britton AJ; Bruni EP; Chen T-W; Dumack K; Fernandez-Mendoza F; Freppaz M; Frey B; Fromin N; Geisen S; Grube M; Guariento E; Guisan A; Ji Q-Q; Jiménez JJ; Maier S; Malard LA; Minor MA; Mc Lean CC; Mitchell EAD; Peham T; Pizzolotto R; Taylor AFS; Vernon P; van Tol JJ; Wu D; Wu Y; Xie Z; Weber B; Illmer P; Seeber JBiological diversity in mountain ecosystems has been increasingly studied over the last decade. This is also the case for mountain soils, but no study to date has provided an overall synthesis of the current state of knowledge. Here we fill this gap with a first global analysis of published research on cryptogams, microorganisms, and fauna in mountain soils above the treeline, and a structured synthesis of current knowledge. Based on a corpus of almost 1400 publications and the expertise of 37 mountain soil scientists worldwide, we summarise what is known about the diversity and distribution patterns of each of these organismal groups, specifically along elevation, and provide an overview of available knowledge on the drivers explaining these patterns and their changes. In particular, we document an elevation-dependent decrease in faunal diversity above the treeline, while for cryptogams there is an initial increase above the treeline, followed by a decrease towards the nival belt. Thus, our data confirm the key role that elevation plays in shaping the biodiversity and distribution of these organisms in mountain soils. The response of prokaryote diversity to elevation, in turn, was more diverse, whereas fungal diversity appeared to be substantially influenced by plants. As far as available, we describe key characteristics, adaptations, and functions of mountain soil species, and despite a lack of ecological information about the uncultivated majority of prokaryotes, fungi, and protists, we illustrate the remarkable and unique diversity of life forms and life histories encountered in alpine mountain soils. By applying rule- as well as pattern-based literature-mining approaches and semi-quantitative analyses, we identified hotspots of mountain soil research in the European Alps and Central Asia and revealed significant gaps in taxonomic coverage, particularly among biocrusts, soil protists, and soil fauna. We further report thematic priorities for research on mountain soil biodiversity above the treeline and identify unanswered research questions. Building upon the outcomes of this synthesis, we conclude with a set of research opportunities for mountain soil biodiversity research worldwide. Soils in mountain ecosystems above the treeline fulfil critical functions and make essential contributions to life on land. Accordingly, seizing these opportunities and closing knowledge gaps appears crucial to enable science-based decision making in mountain regions and formulating laws and guidelines in support of mountain soil biodiversity conservation targets.Item Antibiotic and Heavy Metal Resistance in Bacteria from Contaminated Agricultural Soil: Insights from a New Zealand Airstrip(MDPI (Basel, Switzerland), 2025-02) Heydari A; Kim ND; Biggs PJ; Horswell J; Gielen GJHP; Siggins A; Bromhead C; Meza-Alvarado JC; Palmer BR; Abia ALKBACKGROUND/OBJECTIVES: Agricultural soils accumulate inorganic contaminants from the application of phosphate fertilisers. An airstrip located at Belmont Regional Park (BRP), near Wellington, New Zealand, has been found to have a gradient of cadmium contamination due to spillage of superphosphate fertiliser. METHODS: Soil samples from the BRP airstrip with a gradient of cadmium contamination, were used as a novel source to explore bacterial communities' resistance to heavy metals (HMs) and any co-selected antibiotic (Ab) resistance. RESULTS: Differences between BRP soil samples with higher levels of HMs compared to those with lower HM concentrations showed significantly more bacterial isolates resistant to both HMs (40.6% versus 63.1% resistant to 0.01 mM CdCl2, p < 0.05) and Abs (23.4% versus 37.8% resistant to 20 μg/mL tetracycline, p < 0.05) in soils with higher initial levels of HMs (1.14 versus 7.20 mg kg-1 Cd). Terminal restriction fragment length polymorphism (TRFLP) and 16S rDNA next-generation sequencing profiling investigated changes in HM-induced bacterial communities. Significant differences were observed among the bacterial community structures in the selected BRP soil samples. Conjugative transfer of cadmium resistance from 23-38% of cadmium-resistant isolates to a characterised recipient bacterial strain in vitro suggested many of these genes were carried by mobile genetic elements. Transconjugants were also resistant to zinc, mercury, and Abs. Higher levels of HMs in soil correlated with increased resistance to HMs, Abs, and elevated levels of HMs thus disturbed the bacterial community structure in BRP soil significantly. CONCLUSIONS: These findings suggest that HM contamination of agricultural soil can select for Ab resistance in soil bacteria with potential risks to human and animal health.Item The Classification and Evolution of Bacterial Cross-Feeding(Frontiers Media S.A., 2019-05-14) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC; Harcombe WBacterial feeding has evolved toward specific evolutionary niches and the sources of energy differ between species and strains. Although bacteria fundamentally compete for nutrients, the excreted products from one strain may be the preferred energy source or a source of essential nutrients for another strain. The large variability in feeding preferences between bacterial strains often provides for complex cross-feeding relationships between bacteria, particularly in complex environments such as the human lower gut, which impacts on the host's digestion and nutrition. Although a large amount of information is available on cross-feeding between bacterial strains, it is important to consider the evolution of cross-feeding. Adaptation to environmental stimuli is a continuous process, thus understanding the evolution of microbial cross-feeding interactions allows us to determine the resilience of microbial populations to changes to this environment, such as changes in nutrient supply, and how new interactions might emerge in the future. In this review, we provide a framework of terminology dividing bacterial cross-feeding into four forms that can be used for the classification and analysis of cross-feeding dynamics. Under the proposed framework, we discuss the evolutionary origins for the four forms of cross-feeding and factors such as spatial structure that influence their emergence and subsequent persistence. This review draws from both the theoretical and experimental evolutionary literature to provide a cross-disciplinary perspective on the evolution of different types of cross-feeding.Item Population Structure and Antimicrobial Resistance in Campylobacter jejuni and C. coli Isolated from Humans with Diarrhea and from Poultry, East Africa.(Centers for Disease Control and Prevention, 2024-10) French NP; Thomas KM; Amani NB; Benschop J; Bigogo GM; Cleaveland S; Fayaz A; Hugho EA; Karimuribo ED; Kasagama E; Maganga R; Melubo ML; Midwinter AC; Mmbaga BT; Mosha VV; Mshana FI; Munyua P; Ochieng JB; Rogers L; Sindiyo E; Swai ES; Verani JR; Widdowson M-A; Wilkinson DA; Kazwala RR; Crump JA; Zadoks RNCampylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.Item The effect of three different preservatives on the numbers and types of bacteria, Brix percentage, pH and nutritional composition of bovine colostrum sourced from New Zealand dairy farms(Taylor and Francis Group, 2024-09-02) Cuttance EL; Mason WA; Cranefield S; Laven RAAIMS: To investigate the effect of preservation by addition of yoghurt starter, potassium sorbate and citric acid on counts of aerobic bacteria, Lactobacillus spp., Streptococcus thermophilus and coliforms, Brix percentage, pH, protein, fat and anhydrous lactose concentrations at 0, 7 and 14 days after collection for colostrum stored at ambient temperature. METHOD: Approximately 2 L of first milking colostrum was collected from 10 farms in the Waikato region. Following mixing, it was split into five 400-mL sub-samples and allocated randomly to a control (two sub-samples), or treatment with yoghurt, potassium sorbate, or citric acid preservative. Throughout the trial samples remained in the laboratory at ambient temperature with the lids slightly ajar, and were stirred daily for 15-30 seconds using a sterile spatula. Sub-samples were tested on Days 0, 7 and 14. On Days 0 and 14 aerobic bacteria (by aerobic plate count (APC)), Lactobacillus spp., coliforms and Streptococcus thermophilus counts, pH, Brix percentage, protein, fat and anhydrous lactose were measured. On Day 7 only bacterial counts were completed.The data were analysed using non-parametric clustered bootstrap sampling to estimate the effect of treatment, time, and their interaction on the outcome variables. RESULTS: Compared to control samples, on Day 7 the APC for potassium sorbate (1.0 (90% CI = 0.6-1.6) × 108 cfu/mL) was approximately seven-fold lower than for yoghurt (7.3 (90% CI = 4.1-11) × 108 cfu/mL), and approximately three-fold lower than citric acid (3.2 (90% CI = 0.2-4.3) × 108 cfu/mL) remaining low to Day 14. All preservatives reduced coliform growth compared to control samples at Day 7 but growth was lower for potassium sorbate than the other preservatives. For Lactobacillus spp., at Day 7, samples with yoghurt preservative had greater counts than the other two preservatives. Potassium sorbate reduced growth of S. thermophilus compared to the other treatments, especially at Day 7, with 7-10 times fewer S. thermophilus per mL compared to the other three groups. All groups showed an obvious acidification over time, with very little variation within days and treatment groups. There was no evidence for change in fat or protein percentage over time regardless of treatment. CONCLUSION AND CLINICAL RELEVANCE: Aerobic and coliform bacteria proliferate extensively in unpreserved colostrum. All preservatives decreased coliform counts compared to un-preserved colostrum, but potassium sorbate was more effective at decreasing both coliforms and aerobic bacteria than either yoghurt or citric acid.Item Isolation of Aerobic Bacterial Species Associated with Palpable Udder Defects in Non-Dairy Ewes.(MDPI (Basel, Switzerland), 2024-08-09) Zeleke MM; Kenyon PR; Flay KJ; Aberdein D; Pain SJ; Velathanthiri N; Ridler AL; Zecconi AThe objectives of these studies were to identify associations between udder half defects (hard or lump) and bacteria isolated from milk or mammary tissue swabs, to compare with samples from normal udder halves at different physiological time points and to compare bacterial species isolated via milk and swabs of mammary tissue from within the same udder halves. A total of 1054 samples were aseptically collected from each udder half of 199 non-dairy breed (Romney) ewes from three different studies (Study A, n = 77; Study B, n = 74; and Study C, n = 48). Conventional bacterial culture and MALDI-ToF mass spectrometry were used for bacterial identification. Of the 225 samples from which bacteria were isolated, Mannheimia haemolytica and Streptococcus uberis were the dominantly identified species from defective udder halves, whereas coagulase-negative staphylococcus (CNS) species, mostly Staphylococcus simulans and Staphylococcus chromogenes, were more frequently isolated from normal udder halves. The ongoing presence of bacterial species over time was variable, although less frequently identified species showed less stability over time. A very high agreement (91.5%) of bacterial species identified was observed between the mammary tissue swab and udder half milk samples during post-weaning. In summary, palpable udder half defects were associated with bacterial positivity, and the ongoing presence of the bacteria over time was dependent on the species involved. Hence, culling ewes with palpable udder half defects that had more stable bacterial species could contribute to reducing the recurrence of palpable defects or mastitis.Item The classification and evolution of bacterial cross-feeding(Frontiers Media S.A., 2019-01-01) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC; Harcombe WBacterial feeding has evolved toward specific evolutionary niches and the sources of energy differ between species and strains. Although bacteria fundamentally compete for nutrients, the excreted products from one strain may be the preferred energy source or a source of essential nutrients for another strain. The large variability in feeding preferences between bacterial strains often provides for complex cross-feeding relationships between bacteria, particularly in complex environments such as the human lower gut, which impacts on the host's digestion and nutrition. Although a large amount of information is available on cross-feeding between bacterial strains, it is important to consider the evolution of cross-feeding. Adaptation to environmental stimuli is a continuous process, thus understanding the evolution of microbial cross-feeding interactions allows us to determine the resilience of microbial populations to changes to this environment, such as changes in nutrient supply, and how new interactions might emerge in the future. In this review, we provide a framework of terminology dividing bacterial cross-feeding into four forms that can be used for the classification and analysis of cross-feeding dynamics. Under the proposed framework, we discuss the evolutionary origins for the four forms of cross-feeding and factors such as spatial structure that influence their emergence and subsequent persistence. This review draws from both the theoretical and experimental evolutionary literature to provide a cross-disciplinary perspective on the evolution of different types of cross-feeding.Item Hydrogen cross-feeders of the human gastrointestinal tract.(Taylor & Francis Group, 2019-01-01) Smith NW; Shorten PR; Altermann EH; Roy NC; McNabb WCHydrogen plays a key role in many microbial metabolic pathways in the human gastrointestinal tract (GIT) that have an impact on human nutrition, health and wellbeing. Hydrogen is produced by many members of the GIT microbiota, and may be subsequently utilized by cross-feeding microbes for growth and in the production of larger molecules. Hydrogenotrophic microbes fall into three functional groups: sulfate-reducing bacteria, methanogenic archaea and acetogenic bacteria, which can convert hydrogen into hydrogen sulfide, methane and acetate, respectively. Despite different energy yields per molecule of hydrogen used between the functional groups, all three can coexist in the human GIT. The factors affecting the numerical balance of hydrogenotrophs in the GIT remain unconfirmed. There is increasing evidence linking both hydrogen sulfide and methane to GIT diseases such as irritable bowel syndrome, and strategies for the mitigation of such health problems through targeting of hydrogenotrophs constitute an important field for further investigation.Item Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.(Microbiology Society, 2023-05-12) Mahoney-Kurpe SC; Palevich N; Noel SJ; Gagic D; Biggs PJ; Soni P; Reid PM; Koike S; Kobayashi Y; Janssen PH; Attwood GT; Moon CDTwo strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order 'Christensenellales', were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6-99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order 'Christensenellales'. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.Item Internal Transcribed Spacer and 16S Amplicon Sequencing Identifies Microbial Species Associated with Asbestos in New Zealand(MDPI (Basel, Switzerland), 2023-03-16) Doyle E; Blanchon D; Wells S; de Lange P; Lockhart P; Waipara N; Manefield M; Wallis S; Berry T-A; Henriques IInhalation of asbestos fibres can cause lung inflammation and the later development of asbestosis, lung cancer, and mesothelioma, and the use of asbestos is banned in many countries. In most countries, large amounts of asbestos exists within building stock, buried in landfills, and in contaminated soil. Mechanical, thermal, and chemical treatment options do exist, but these are expensive, and they are not effective for contaminated soil, where only small numbers of asbestos fibres may be present in a large volume of soil. Research has been underway for the last 20 years into the potential use of microbial action to remove iron and other metal cations from the surface of asbestos fibres to reduce their toxicity. To access sufficient iron for metabolism, many bacteria and fungi produce organic acids, or iron-chelating siderophores, and in a growing number of experiments these have been found to degrade asbestos fibres in vitro. This paper uses the internal transcribed spacer (ITS) and 16S amplicon sequencing to investigate the fungal and bacterial diversity found on naturally-occurring asbestos minerals, asbestos-containing building materials, and asbestos-contaminated soils with a view to later selectively culturing promising species, screening them for siderophore production, and testing them with asbestos fibres in vitro. After filtering, 895 ITS and 1265 16S amplicon sequencing variants (ASVs) were detected across the 38 samples, corresponding to a range of fungal, bacteria, cyanobacterial, and lichenized fungal species. Samples from Auckland (North Island, New Zealand) asbestos cement, Auckland asbestos-contaminated soils, and raw asbestos rocks from Kahurangi National Park (South Island, New Zealand) were comprised of very different microbial communities. Five of the fungal species detected in this study are known to produce siderophores.