ITS-RFLP and sequence analysis of endophytes from Acianthus, Caladenia and Pterostylis (Orchidaceae) in southeastern Queensland

We used ITS-RFLP and sequence analysis to determine the identities of the fungal endophytes of six terrestrial orchid species from southeastern Queensland, a region previously unexplored in this context. Pure cultures of orchid--colonising fungi were obtained and fungal identities were assessed by means of ITS-PCR, RFLP analysis, sequence comparison, and protocorm colonisation tests. ITS-PCR and RFLP analysis resulted in five main groupings. Sequencing and GenBank comparison of these five groups showed that the fungal endophytes isolated from the three Pterostylis species were probably Thanatephorus species. There was close sequence identity (90%) of the fungus isolated from Acianthus spp. to Epulorhiza repens, suggesting these may be the same fungal species. However, that only E. repens succeeded in colonising protocorms of Thelymitra pauciflora suggests these may be different species of Epulorhiza. Analysis of the ITS and LSU sequences of the fungus isolated from Caladenia carnea showed high identities with a sequence from a Sebacina vermifera originally isolated from Caladenia dilatata. These results show that there is specificity for fungal partners within the orchid genera Acianthus, Caladenia and Pterostylis.

Organic Matter Amendment and Plant Colonization Drive Mineral Weathering, Organic Carbon Sequestration, and Water-Stable Aggregation in Magnetite Fe Ore Tailings

The formation of water-stable aggregates in finely textured and polymineral magnetite Fe ore tailings is one of the critical processes in eco-engineering tailings into soil-like substrates as a new way to rehabilitate the tailings. Organic matter (OM) amendment and plant colonization are considered to be effective in enhancing water-stable aggregation, but the underlying mechanisms have not yet been elucidated. The present study aimed to characterize detailed changes in physicochemistry, Fe-bearing mineralogy, and organo-mineral interactions in magnetite Fe ore tailings subject to the combined treatments of OM amendment and plant colonization, by employing various microspectroscopic methods, including synchrotron-based X-ray absorption fine structure spectroscopy and nanoscale secondary ion mass spectroscopy. The results indicated that OM amendment and plant colonization neutralized the tailings' alkaline pH and facilitated water-stable aggregate formation. The resultant aggregates were consequences of ligand-promoted bioweathering of primary Fe-bearing minerals (mainly biotite-like minerals) and the formation of secondary Fe-rich mineral gels. Especially, the sequestration of OM (rich in carboxyl, aromatic, and/or carbonyl C) by Fe-rich minerals via ligand-exchange and/or hydrophobic interactions contributed to the aggregation. These findings have uncovered the processes and mechanisms of water-stable aggregate formation driven by OM amendment and plant colonization in alkaline Fe ore tailings, thus providing important basis for eco-engineered pedogenesis in the tailings.

Carbon and nitrogen supply to the underground orchid, Rhizanthella gardneri

*Rhizanthella gardneri is a rare and fully subterranean orchid that is presumably obligately mycoheterotrophic. R. gardneri is thought to be linked via a common mycorrhizal fungus to co-occurring autotrophic shrubs, but there is no experimental evidence to support this supposition. *We used compartmentalized microcosms to investigate the R. gardneri tripartite relationship. (13)CO(2) was applied to foliage of Melaleuca scalena plants and [(13)C-(15)N]glycine was fed to the common mycorrhizal fungus, and both sources traced to R. gardneri plants. *In our microcosm trial, up to 5% of carbon (C) fed as (13)CO(2) to the autotrophic shrub was transferred to R. gardneri. R. gardneri also readily acquired soil C and nitrogen (N), where up to 6.2% of C and 22.5% of N fed as labelled glycine to soil was transferred via the fungus to R. gardneri after 240 h. *Our study confirms that R. gardneri is mycoheterotrophic and acquires nutrients via mycorrhizal fungus connections from an ectomycorrhizal autotrophic shrub and directly from the soil via the same fungus. This connection with a specific fungus is key to explaining why R. gardneri occurs exclusively under certain Melaleuca species at a very limited number of sites in Western Australia.

Ecological engineering of iron ore tailings into useable soils for sustainable rehabilitation

Ecological engineering of soil formation in tailings is an emerging technology toward sustainable rehabilitation of iron (Fe) ore tailings landscapes worldwide, which requires the formation of well-organized and stable soil aggregates in finely textured tailings. Here, we demonstrate an approach using microbial and rhizosphere processes to progressively drive aggregate formation and development in Fe ore tailings. The aggregates were initially formed through the agglomeration of mineral particles by organic cements derived from microbial decomposition of exogenous organic matter. The aggregate stability was consolidated by colloidal nanosized Fe(III)-Si minerals formed during Fe-bearing primary mineral weathering driven by rhizosphere biogeochemical processes of pioneer plants. From these findings, we proposed a conceptual model for progressive aggregate structure development in the tailings with Fe(III)-Si rich cements as core nuclei. This renewable resource dependent eco-engineering approach opens a sustainable pathway to achieve resilient tailings rehabilitation without resorting to excavating natural soil resources.

Comparing Raman and NanoSIMS for heavy water labeling of single cells

Stable isotope probing (SIP) experiments in conjunction with Raman microspectroscopy (Raman) or nano-scale secondary ion mass spectrometry (NanoSIMS) are frequently used to explore single cell metabolic activity in pure cultures as well as complex microbiomes. Despite the increasing popularity of these techniques, the comparability of isotope incorporation measurements using both Raman and NanoSIMS directly on the same cell remains largely unexplored. This knowledge gap creates uncertainty about the consistency of single-cell SIP data obtained independently from each method. Here, we conducted a comparative analysis of 543 Escherichia coli cells grown in M9 minimal medium in the absence or presence of heavy water ( 2 H 2 O) using correlative Raman and NanoSIMS measurements to quantify the results between the two approaches. We demonstrate that Raman and NanoSIMS yield highly comparable measurements of 2 H incorporation, with varying degrees of similarity based on the mass ratios analyzed using NanoSIMS. The 12 C 2 H/ 12 C 1 H and 12 C 2 2 H/ 12 C 2 1 H mass ratios provide targeted measurements of C-H bonds but may suffer from biases and background interference, while the 2 H/ 1 H ratio captures all hydrogen with lower detection limits, making it suitable for applications requiring comprehensive 2 H quantification. Importantly, despite its higher mass resolution requirements, the use of C 2 2 H/C 2 1 H may be a viable alternative to using C 2 H/C 1 H due to lower background and higher overall count rates. Furthermore, using an empirical approach to determining Raman wavenumber ranges via the 2 nd derivative improved the data equivalency of 2 H quantification between Raman and NanoSIMS, highlighting its potential for enhancing cross-technique comparability. These findings provide a robust framework for leveraging both techniques, enabling informed experimental design and data interpretation. By enhancing cross-technique comparability, this work advances SIP methodologies for investigating microbial metabolism and interactions in diverse systems.

Importance

Accurate and reliable measurements of cellular properties are fundamental to understanding the function and activity of microbes. This study addresses to what extent Raman microspectroscopy and nano-scale secondary ion mass spectrometry (NanoSIMS) measurements of single cell anabolic activity can be compared. Here, we study the relationship of the incorporation of a stable isotope ( 2 H through incorporation of 2 H 2 O) as determined by the two techniques and calculate a correlation coefficient to support the use of either technique when analyzing cells incubated with 2 H 2 O. The ability to discern between the comparative strengths and limitations of these techniques is invaluable in refining experimental protocols, enhancing data comparability between studies, data interpretation, and ultimately advancing the quality and reliability of outcomes in microbiome research.