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The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.

Self-incompatibility (SI) in plants has evolved independently multiple times and S -RNase-based gametophytic self-incompatibility (GSI) is most common. The Rosaceae family possesses both self-recognition ( Prunus ) and nonself-recognition ( Malus ) GSI systems, and the latter is widespread in flowering plants. Gillenia trifoliata is a Rosaceae species related to Prunus and Malus , providing utility for understanding SI evolution. Gillenia is sister taxon to Malus , but unlike Malus , has not undergone polyploidisation. In addition, the common ancestor of Gillenia and Prunus is close to the origin of the subfamily. Using a highly contiguous Gillenia genome, orthologous regions to both Malus and Prunus S -loci were identified. Only the Prunus -like S -locus was highly polymorphic and had signatures of a functional S -locus including positive selection of the S -RNase. This suggests a self-recognition system controls SI in Gillenia , and the common ancestors of Gillenia and Prunus , and Gillenia and the apple tribe, likely had a self-recognition SI system. Comparative genomics between Gillenia and Malus suggest apple lost the self-recognition mechanism, and a nonself-recognition mechanism evolved independently from a rudimentary locus with at least one male S -determinant. Repetitive sequences in the Malus -like S -locus in Gillenia may facilitate illegitimate recombination, suggesting putative mechanisms of evolution of nonself-recognition S -loci.

This study was made possible by funding from the Ministry for Business, Innovation and Employment (MBIE) of New Zealand, NIWA Coast and Oceans Food Webs (COES) and Ocean Flows (COOF), and the Royal Society of New Zealand Marsden Fast-track award to MD, and by U.S. National Science Foundation awards OCE- 1756610 and 1756465 to MS and KES.

River biofilms dominated by Phormidium (cyanobacteria) are receiving increased attention worldwide because of a recent expansion in their distribution and their ability to produce neurotoxins leading to animal mortalities. Limited data are available on the composition and structure of bacterial communities (BCs) associated with Phormidium biofilms despite the important role they potentially play in biofilm functioning. By using a high-throughput sequencing approach, we compared the BCs associated with Phormidium biofilms in several sampling sites of the Tarn River (France) and in eight New Zealand rivers. The structure of the BCs from both countries displayed spatial and temporal variations but were well conserved at the order level and 28% of the OTUs containing 90% of the reads were shared by these BCs. This suggests that micro-environmental conditions occurring within thick Phormidium biofilms strongly shape the associated BCs. A strong and significant distance-decay relationship (rp = 0.7; P = 0.001) was found in BCs from New Zealand rivers but the Bray-Curtis dissimilarities between French and New Zealand BCs are in the same order of magnitude of those found between New Zealand BCs. All these findings suggest that local environmental conditions seem to have more impact on BCs than dispersal capacities of bacteria.

Model code is available as a zip file (Supplementary Dataset 6) that includes a Matlab live script, which can be used to generate all figures and summary data in the manuscript. It is also available on GitHub: https://github.com/mstukel/SalpEcosystemEfficiency and on Zenodo: https://doi.org/10.5281/zenodo.12700512.

This paper has heavily relied on the extensive data collected from numerous voyages to the Southern Ocean over a span of 26 years. While it is challenging to individually acknowledge everyone involved, we would like to express our sincere gratitude to the scientific community as a whole. The unwavering dedication of scientists in sharing their data through online repositories showcases the remarkable commitment of the oceanographic community to unravelling the mysteries of intricately complex oceans. I would like to thank Dr. Thomas Ryan-Keogh, Dr. Sandy Thomalla and the SOCCO project for their contributions of pigment data and help. We acknowledge NIWA for providing funding through the NIWA PhD scholarship (CDPS2001) and the University of Otago (Department of Marine Science) for their support throughout the PhD programme. We are also grateful to the New Zealand MBIE Endeavour Programme C01X1710 (Ross-RAMP), Antarctic Science Platform, Project 3 (MBIE contract ANTA1801), MBIE NIWA SSIF (“Structure and function of marine ecosystems”) for financial support. We acknowledge the contribution to this work by the R open-source collective and R Studio.

Background PTI and ETI are the two major defence mechanisms in plants. ETI is triggered by the detection of pathogen effectors, or their activity, in the plant cell and most of the time involves internal receptors known as resistance (R) genes. An increasing number of R genes responsible for recognition of specific effectors have been characterised over the years; however, methods to identify R genes are often challenging and cannot always be translated to crop plants. Results We present a novel method to identify R genes responsible for the recognition of specific effectors that trigger a hypersensitive response (HR) in Nicotiana benthamiana . This method is based on the genome-wide identification of most of the potential R genes of N. benthamiana and a systematic silencing of these potential R genes in a simple transient expression assay. A hairpin-RNAi library was constructed covering 345 R gene candidates of N. benthamiana . This library was then validated using several previously described R genes. Our approach indeed confirmed that Prf, NRC2a/b and NRC3 are required for the HR that is mediated in N. benthamiana by Pto/avrPto (prf, NRC2a/b and NRC3) and by Cf4/avr4 (NRC2a/b and NRC3). We also confirmed that NRG1, in association with N, is required for the Tobacco Mosaic Virus (TMV)-mediated HR in N. benthamiana . Conclusion We present a novel approach combining bioinformatics, multiple-gene silencing and transient expression assay screening to rapidly identify one-to-one relationships between pathogen effectors and host R genes in N. benthamiana . This approach allowed the identification of previously described R genes responsible for detection of avirulence determinants from Pseudomonas , Cladosporium and TMV, demonstrating that the method could be applied to any effectors/proteins originating from a broad range of plant pathogens that trigger an HR in N. benthamiana . Moreover, with the increasing availability of genome sequences from model and crop plants and pathogens, this approach could be implemented in other plants, accelerating the process of identification and characterization of novel resistance genes.

Phytoplankton are critical to the Antarctic marine food web and associated biological carbon pump, yet long-term shifts in their community composition are poorly understood. Here, using a machine learning framework and combining pigment samples and environmental samples from austral summertime 1997–2023, we show declines in diatoms and increases in haptophytes and cryptophytes across much of Antarctica’s continental shelf. These trends—which are linked to sea ice increases—reversed after 2016, with a rebound in diatoms and a large increase in cryptophytes, coinciding with the loss of sea ice. Significant changes (P < 0.05) across the 25-year dataset include diatom chlorophyll a (chl-a) declines of 0.32 mg chl-a m−3 (~33% of the climatology) and increases for haptophytes and cryptophytes of 0.08 and 0.23 mg chl-a m−3, respectively. The long-term shifts in phytoplankton assemblages could reduce the dominance of the krill-centric food web and diminish the biologically mediated export of carbon to depth, with implications for the global-ocean carbon sink.

Fire blight, caused by the bacterium Erwinia amylovora (Burrill) Winslow et al., is one of the most serious diseases of pear. The development of pear cultivars with a durable resistance is extremely important for effective control of fire blight and is a key objective of most pear breeding programs throughout the world. We phenotyped seedlings from the interspecific pear population PEAR3 (PremP003, P. x bretschneideri x P. communis) x 'Moonglow' (P. communis) for fire blight resistance at two different geographic locations, in France and New Zealand, respectively, employing two local E. amylovora isolates. Using a genetic map constructed with single nucleotide polymorphism (SNP) and microsatellite (SSR) markers previously developed for this segregating population, we detected a major quantitative trait locus (QTL) on linkage group (LG)2 of 'Moonglow' (R-2 = 12.9-34.4 %), which was stable in both environments. We demonstrated that this QTL co-localizes with another major QTL for fire blight resistance previously detected in 'Harrow Sweet' and that the two favorable (i.e., resistant) alleles were not identical by descent. We also identified some smaller effect (R-2 = 8.1-14.8 %) QTLs derived from the susceptible parent PEAR3. We propose SNP and SSR markers linked to the large effect QTL on LG2 as candidates for marker-assisted breeding for fire blight resistance in pear.

Douglas-fir is a conifer species with high and increasing interest for forest industries in both New Zealand and France. Delivery of the best trees to the forest from breeding programs is currently constrained by an inability to effectively and reliably multiply selections through vegetative propagation. Somatic embryogenesis coupled with cryopreservation are essential biotechnology tools in conifers for scaling up variety design and production. The aim of this work was therefore to develop protocols for the initiation and proliferation of Douglas-fir embryogenic cell lines based on modifications of previously published techniques and media available in the public domain, especially successful methods developed for P. radiata at Scion. Three years of initiation experiments have resulted in a simple and efficient protocol. Disinfection of whole cones (instead of seeds) was sufficient to prevent contamination. Immature zygotic embryos were excised from megagametophytes and placed onto a modified Litvay medium (Litvay et al. 1985). At optimal development stages of zygotic embryos, the average initiation percentage of embryogenic tissue was 69.3% when our most effective protocol was used. Proliferation of initiated cell lines on a Glitz formulation was challenging, with a high percentage of cell lines composed of a mixture of both embryonal masses and callus. 2,4-D at a lower concentration reduced the number of such mixed lines. Repeated liquid suspension and subculture of the embryogenic parts of the tissue was an efficient means to increase the number of embryogenic cell lines with sustained proliferation. Maltose added to the proliferation medium in place of sucrose improved fresh mass gain and consistently increased early somatic embryo patterning and growth. A sample of proliferating cell lines was successfully cryopreserved, thawed and somatic embryos were matured and germinated from these lines. The method may be of practical interest and provide new opportunities to realise increased genetic gain in this species through the clonal-assisted deployment of the best genetic material in both New Zealand and France.