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The eastern tropical Pacific (ETP) bears one of the largest perennial OMZs, which is strongly influenced by the recurring El Ni\u00f1o Southern Oscillation (ENSO). However, how microbial diversity and nitrogen cycling respond to oxygen variability under comparable ENSO conditions remains unclear. Here, we applied metagenomics to analyze changes in microbial communities across a dissolved oxygen (DO) gradient from oxic to suboxic conditions in the ETP during the 2022 La Ni\u00f1a event and compared our findings to the\n                      <jats:italic toggle=\"yes\">Tara Oceans<\/jats:italic>\n                      data set from the same region during the 2011 La Ni\u00f1a. In 2022, we observed a decline in microbial alpha diversity and abundance, coupled with an increase in nitrogen metabolism genes as DO decreases. The relative abundance of many dominant microbes shifted at a DO threshold of 80 \u03bcmol kg\n                      <jats:sup>\u22121<\/jats:sup>\n                      , while dominant nitrogen cycle genes varied under different DO thresholds (120, 20, 5 \u03bcmol kg\n                      <jats:sup>\u22121<\/jats:sup>\n                      ). Despite the 11-year interval between sampling efforts, microbial alpha diversity was similar between 2011 and 2022. We observed a significant reduction of SAR11 and an increase of Poseidoniia in 2022 compared with 2011. While certain nitrogen cycling genes differed in relative abundance in a depth-dependent manner, overall functional group composition was largely consistent, with spatial variation exceeding interannual differences. Overall, our study presents a comprehensive examination of possible shifts of microbial diversity, community, and their potential for nitrogen cycling under deoxygenation during two La Ni\u00f1a years.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>The eastern tropical Pacific oxygen minimum zones (OMZs), largely impacted by the natural climate cycle\u2014El Ni\u00f1o-Southern Oscillation, are predicted to continually expand while their core may shrink. While deoxygenation is known to profoundly influence microbial ecosystems, how microbial diversity, composition, and nitrogen cycling would shift across oxic\/hypoxic\/suboxic gradients, and its association with ENSO dynamics remains poorly understood. We surveyed microbial communities under two La Ni\u00f1a years with an 11-year gap and found that vertical variability is more critical than temporal variations for both microbial diversity and microbe-mediated nitrogen pathways, as only slight differences in microbial diversity and nitrogen cycles were detected between the two studied years despite ENSO dynamics, which might have disrupted the system among the 11 years. Moreover, we identified oxygen thresholds causing dominant microbes and potential nitrogen pathways to shift, thus helping to improve prediction on how various microbes and nitrogen pathways might respond to further deoxygenation.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00893-26","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:01:22Z","timestamp":1789995682000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Microbial diversity and nitrogen cycling across oxygen gradients in the eastern tropical Pacific during two La Ni\u00f1a years"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4576-8131","authenticated-orcid":true,"given":"Peihang","family":"Xu","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03yrrjy16","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biology, University of Southern Denmark","place":["Odense, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damian L.","family":"Ar\u00e9valo-Mart\u00ednez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03xh9nq73","id-type":"ROR","asserted-by":"publisher"}],"name":"Leibniz Institute for Baltic Sea Research Warnem\u00fcnde","place":["Rostock, Germany"]},{"name":"Chemical Oceanography, GEOMAR Helmholtz Center for Ocean Research Kiel","place":["Kiel, 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