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Structure peer review to make it more robust

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In February, I received two peer-review reports for a manuscript I’d submitted to a journal. One report contained 3 comments, the other 11. Apart from one point, all the feedback was different. It focused on expanding the discussion and some methodological details — there were no remarks about the study’s objectives, analyses or limitations.

My co-authors and I duly replied, working under two assumptions that are common in scholarly publishing: first, that anything the reviewers didn’t comment on they had found acceptable for publication; second, that they had the expertise to assess all aspects of our manuscript. But, as history has shown, those assumptions are not always accurate (see Lancet 396, 1056; 2020). And through the cracks, inaccurate, sloppy and falsified research can slip.

As co-editor-in-chief of the journal Research Integrity and Peer Review (an open-access journal published by BMC, which is part of Springer Nature), I’m invested in ensuring that the scholarly peer-review system is as trustworthy as possible. And I think that to be robust, peer review needs to be more structured. By that, I mean that journals should provide reviewers with a transparent set of questions to answer that focus on methodological, analytical and interpretative aspects of a paper.

For example, editors might ask peer reviewers to consider whether the methods are described in sufficient detail to allow another researcher to reproduce the work, whether extra statistical analyses are needed, and whether the authors’ interpretation of the results is supported by the data and the study methods. Should a reviewer find anything unsatisfactory, they should provide constructive criticism to the authors. And if reviewers lack the expertise to assess any part of the manuscript, they should be asked to declare this.

Other aspects of a study, such as novelty, potential impact, language and formatting, should be handled by editors, journal staff or even machines, reducing the workload for reviewers.

The list of questions reviewers will be asked should be published on the journal’s website, allowing authors to prepare their manuscripts with this process in mind. And, as others have argued before, review reports should be published in full. This would allow readers to judge for themselves how a paper was assessed, and would enable researchers to study peer-review practices.

To see how this works in practice, since 2022 I’ve been working with the publisher Elsevier on a pilot study of structured peer review in 23 of its journals, covering the health, life, physical and social sciences. The preliminary results indicate that, when guided by the same questions, reviewers made the same initial recommendation about whether to accept, revise or reject a paper 41% of the time, compared with 31% before these journals implemented structured peer review. Moreover, reviewers’ comments were in agreement about specific parts of a manuscript up to 72% of the time (M. Malički and B. Mehmani Preprint at bioRxiv https://doi.org/mrdv; 2024). In my opinion, reaching such agreement is important for science, which proceeds mainly through consensus.

I invite editors and publishers to follow in our footsteps and experiment with structured peer reviews. Anyone can trial our template questions (see go.nature.com/4ab2ppc), or tailor them to suit specific fields or study types. For instance, mathematics journals might also ask whether referees agree with the logic or completeness of a proof. Some journals might ask reviewers if they have checked the raw data or the study code. Publications that employ editors who are less embedded in the research they handle than are academics might need to include questions about a paper’s novelty or impact.

Scientists can also use these questions, either as a checklist when writing papers or when they are reviewing for journals that don’t apply structured peer review.

Some journals — including Proceedings of the National Academy of Sciences, the PLOS family of journals, F1000 journals and some Springer Nature journals — already have their own sets of structured questions for peer reviewers. But, in general, these journals do not disclose the questions they ask, and do not make their questions consistent. This means that core peer-review checks are still not standardized, and reviewers are tasked with different questions when working for different journals.

Some might argue that, because different journals have different thresholds for publication, they should adhere to different standards of quality control. I disagree. Not every study is groundbreaking, but scientists should view quality control of the scientific literature in the same way as quality control in other sectors: as a way to ensure that a product is safe for use by the public. People should be able to see what types of check were done, and when, before an aeroplane was approved as safe for flying. We should apply the same rigour to scientific research.

Ultimately, I hope for a future in which all journals use the same core set of questions for specific study types and make all of their review reports public. I fear that a lack of standard practice in this area is delaying the progress of science.

Competing Interests

M.M. is co-editor-in-chief of the Research Integrity and Peer Review journal that publishes signed peer review reports alongside published articles. He is also the chair of the European Association of Science Editors Peer Review Committee.

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Scientists discover first algae that can fix nitrogen — thanks to a tiny cell structure

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1000x magnification micrograph of Braarudospharea bigelowii cell.

A Braarudosphaera bigelowii cell magnified 1,000-fold.Credit: Tyler Coale

Researchers have discovered a type of organelle, a fundamental cellular structure, that can turn nitrogen gas into a form that is useful for cell growth.

The discovery of the structure, called a nitroplast, in algae could bolster efforts to genetically engineer plants to convert, or ‘fix’, their own nitrogen, which could boost crop yields and reduce the need for fertilizers. The work was published in Science on 11 April1.

“The textbooks say nitrogen fixation only occurs in bacteria and archaea,” says ocean ecologist Jonathan Zehr at the University of California, Santa Cruz, a co-author of the study. This species of algae is the “first nitrogen-fixing eukaryote”, he adds, referring to the group of organisms that includes plants and animals.

In 2012, Zehr and his colleagues reported that the marine algae Braarudosphaera bigelowii interacted closely with a bacterium called UCYN-A that seemed to live in, or on, the algal cells2. The researchers hypothesised that UCYN-A converts nitrogen gas into compounds that the algae use to grow, such as ammonia. In return, the bacteria were thought to gain a carbon-based energy source from the algae.

But in the latest study, Zehr and his colleagues conclude that UCYN-A should be classed as organelles inside the algae, rather than as a separate organism. According to genetic analysis from a previous study, ancestors of the algae and bacteria entered a symbiotic relationship around 100 million years ago, says Zehr. Eventually, this gave rise to the nitroplast organelle, now seen in B. bigelowii.

Defining organelles

Researchers use two key criteria to decide whether a bacterial cell has become an organelle in a host cell. First, the cell structure in question must be passed down through generations of the host cell. Second, the structure must be reliant on proteins provided by the host cell.

By imaging dozens of algae cells at various stages of cell division, the team found that the nitroplast splits in two just before the whole algae cell divides. In this way, one nitroplast is passed down from the parent cell to its offspring, as happens with other cell structures.

Next, the researchers found that the nitroplast gets the proteins it needs to grow from the wider algae cell. The nitroplast itself — which makes up more than 8% of the volume of each host cell — lacks key proteins required for photosynthesis and making genetic material, says Zehr. “A lot of these proteins [from the algae] are just filling those gaps in metabolism,” he says.

The discovery was made possible thanks to work by study author Kyoko Hagino at Kochi University in Japan, who spent around a decade fine-tuning a way to grow the algae in the lab — which allowed it to be studied in more detail, says Zehr.

“It’s quite remarkable,” says Siv Andersson, who studies how organelles evolve at Uppsala University in Sweden. “They really see all these hallmarks that we think are characteristic of organelles.”

Upgraded plants

Understanding how the nitroplast interacts with its host cell could support efforts to engineer crops that can fix their own nitrogen, says Zehr. This would reduce the need for nitrogen-based fertilizers and avoid some of the environmental damage they cause. “The tricks that are involved in making this system work could be used in engineering land plants,” he says.

“Crop yields are majorly limited by availability of nitrogen,” says Eva Nowack, who studies symbiotic bacteria at the Heinrich Heine University Düsseldorf in Germany. “Having a nitrogen-fixing organelle in a crop plant would be, of course, fantastic.” But introducing this ability into plants will be no easy feat, she warns. Plant cells containing the genetic code for the nitroplast would need to be engineered in such a way that the genes were transferred stably from generation to generation, for example. “That would be the most difficult thing to do,” she says.

“It’s both a pleasure and very impressive to see this work build up to what is certainly a major stepping stone in understanding,” says Jeffrey Elhai, a cell biologist at Virginia Commonwealth University in Richmond, Vriginia.

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